diff --git a/java/lance-jni/src/blocking_dataset.rs b/java/lance-jni/src/blocking_dataset.rs
index 889c3e572eb..0e4d21dee98 100644
--- a/java/lance-jni/src/blocking_dataset.rs
+++ b/java/lance-jni/src/blocking_dataset.rs
@@ -59,7 +59,7 @@ use lance_namespace::LanceNamespace;
 use lance_table::io::commit::CommitHandler;
 use lance_table::io::commit::external_manifest::ExternalManifestCommitHandler;
 use lance_table::io::commit::{ManifestLocation, ManifestNamingScheme};
-use std::collections::HashMap;
+use std::collections::{HashMap, HashSet};
 use std::future::IntoFuture;
 use std::iter::empty;
 use std::sync::Arc;
@@ -3438,6 +3438,14 @@ fn extract_cleanup_policy(env: &mut JNIEnv<'_>, jpolicy: &JObject) -> Result<Cle
 
     let before_version = env.get_optional_u64_from_method(jpolicy, "getBeforeVersion")?;
 
+    let versions = env.get_optional_from_method(jpolicy, "getVersions", |env, list_obj| {
+        let mut versions = HashSet::new();
+        for version in env.get_longs(&list_obj)? {
+            versions.insert(version as u64);
+        }
+        Ok(versions)
+    })?;
+
     let delete_unverified = env
         .get_optional_from_method(jpolicy, "getDeleteUnverified", |env, obj| {
             Ok(env.call_method(obj, "booleanValue", "()Z", &[])?.z()?)
@@ -3461,6 +3469,7 @@ fn extract_cleanup_policy(env: &mut JNIEnv<'_>, jpolicy: &JObject) -> Result<Cle
     Ok(CleanupPolicy {
         before_timestamp,
         before_version,
+        versions,
         delete_unverified,
         error_if_tagged_old_versions,
         clean_referenced_branches,
diff --git a/java/src/main/java/org/lance/cleanup/CleanupPolicy.java b/java/src/main/java/org/lance/cleanup/CleanupPolicy.java
index 6316f70f1a6..25da8763747 100644
--- a/java/src/main/java/org/lance/cleanup/CleanupPolicy.java
+++ b/java/src/main/java/org/lance/cleanup/CleanupPolicy.java
@@ -13,6 +13,9 @@
  */
 package org.lance.cleanup;
 
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.List;
 import java.util.Optional;
 
 /**
@@ -24,6 +27,7 @@
 public class CleanupPolicy {
   private final Optional<Long> beforeTimestampMillis;
   private final Optional<Long> beforeVersion;
+  private final Optional<List<Long>> versions;
   private final Optional<Boolean> deleteUnverified;
   private final Optional<Boolean> errorIfTaggedOldVersions;
   private final Optional<Boolean> cleanReferencedBranches;
@@ -32,12 +36,14 @@ public class CleanupPolicy {
   private CleanupPolicy(
       Optional<Long> beforeTimestampMillis,
       Optional<Long> beforeVersion,
+      Optional<List<Long>> versions,
       Optional<Boolean> deleteUnverified,
       Optional<Boolean> errorIfTaggedOldVersions,
       Optional<Boolean> cleanReferencedBranches,
       Optional<Long> deleteRateLimit) {
     this.beforeTimestampMillis = beforeTimestampMillis;
     this.beforeVersion = beforeVersion;
+    this.versions = versions;
     this.deleteUnverified = deleteUnverified;
     this.errorIfTaggedOldVersions = errorIfTaggedOldVersions;
     this.cleanReferencedBranches = cleanReferencedBranches;
@@ -56,6 +62,10 @@ public Optional<Long> getBeforeVersion() {
     return beforeVersion;
   }
 
+  public Optional<List<Long>> getVersions() {
+    return versions;
+  }
+
   public Optional<Boolean> getDeleteUnverified() {
     return deleteUnverified;
   }
@@ -76,6 +86,7 @@ public Optional<Long> getDeleteRateLimit() {
   public static class Builder {
     private Optional<Long> beforeTimestampMillis = Optional.empty();
     private Optional<Long> beforeVersion = Optional.empty();
+    private Optional<List<Long>> versions = Optional.empty();
     private Optional<Boolean> deleteUnverified = Optional.empty();
     private Optional<Boolean> errorIfTaggedOldVersions = Optional.empty();
     private Optional<Boolean> cleanReferencedBranches = Optional.empty();
@@ -95,6 +106,12 @@ public Builder withBeforeVersion(long beforeVersion) {
       return this;
     }
 
+    /** Set the exact dataset versions to clean. */
+    public Builder withVersions(List<Long> versions) {
+      this.versions = Optional.of(Collections.unmodifiableList(new ArrayList<>(versions)));
+      return this;
+    }
+
     /** If true, delete unverified data files even if they are recent. */
     public Builder withDeleteUnverified(boolean deleteUnverified) {
       this.deleteUnverified = Optional.of(deleteUnverified);
@@ -123,6 +140,7 @@ public CleanupPolicy build() {
       return new CleanupPolicy(
           beforeTimestampMillis,
           beforeVersion,
+          versions,
           deleteUnverified,
           errorIfTaggedOldVersions,
           cleanReferencedBranches,
diff --git a/java/src/test/java/org/lance/CleanupTest.java b/java/src/test/java/org/lance/CleanupTest.java
index 5fc8ceeaa3f..f6f3f0ef043 100644
--- a/java/src/test/java/org/lance/CleanupTest.java
+++ b/java/src/test/java/org/lance/CleanupTest.java
@@ -54,6 +54,31 @@ public void testCleanupBeforeVersion(@TempDir Path tempDir) {
     }
   }
 
+  @Test
+  public void testCleanupSpecificVersions(@TempDir Path tempDir) {
+    String datasetPath = tempDir.resolve("test_dataset_for_cleanup").toString();
+    try (RootAllocator allocator = new RootAllocator(Long.MAX_VALUE)) {
+      TestUtils.SimpleTestDataset testDataset =
+          new TestUtils.SimpleTestDataset(allocator, datasetPath);
+
+      testDataset.createEmptyDataset().close();
+
+      testDataset.write(1, 10).close();
+      testDataset.write(2, 10).close();
+
+      try (Dataset dataset = testDataset.write(3, 10)) {
+        assertEquals(4, dataset.listVersions().size());
+
+        RemovalStats stats =
+            dataset.cleanupWithPolicy(CleanupPolicy.builder().withVersions(List.of(2L)).build());
+
+        assertEquals(1L, stats.getOldVersions());
+        assertEquals(3, dataset.listVersions().size());
+        assertTrue(dataset.listVersions().stream().noneMatch(version -> version.getId() == 2L));
+      }
+    }
+  }
+
   @Test
   public void testExplainCleanupBeforeVersion(@TempDir Path tempDir) {
     String datasetPath = tempDir.resolve("test_dataset_for_cleanup").toString();
diff --git a/python/python/lance/dataset.py b/python/python/lance/dataset.py
index e386e6cb854..0be922aa889 100644
--- a/python/python/lance/dataset.py
+++ b/python/python/lance/dataset.py
@@ -3143,6 +3143,7 @@ def cleanup_old_versions(
         delete_unverified: bool = False,
         error_if_tagged_old_versions: bool = True,
         delete_rate_limit: Optional[int] = None,
+        versions: Optional[List[int]] = None,
     ) -> CleanupStats:
         """
         Cleans up old versions of the dataset.
@@ -3188,8 +3189,13 @@ def cleanup_old_versions(
             deletions run at full speed. Set this to a positive integer to avoid
             hitting object store request rate limits (e.g. S3 HTTP 503 SlowDown).
             For example, ``delete_rate_limit=100`` limits to 100 operations/second.
+
+        versions: list[int], optional
+            Clean up only the specified dataset versions. The current version is
+            never removed, and tagged versions are still protected by
+            ``error_if_tagged_old_versions``.
         """
-        if older_than is None and retain_versions is None:
+        if older_than is None and retain_versions is None and versions is None:
             older_than = timedelta(days=14)
 
         return self._ds.cleanup_old_versions(
@@ -3198,6 +3204,7 @@ def cleanup_old_versions(
             delete_unverified,
             error_if_tagged_old_versions,
             delete_rate_limit,
+            versions,
         )
 
     def explain_cleanup_old_versions(
@@ -3208,6 +3215,7 @@ def explain_cleanup_old_versions(
         delete_unverified: bool = False,
         error_if_tagged_old_versions: bool = True,
         delete_rate_limit: Optional[int] = None,
+        versions: Optional[List[int]] = None,
         include_files: bool = False,
         max_files: int = 1000,
     ) -> CleanupExplanation:
@@ -3235,6 +3243,9 @@ def explain_cleanup_old_versions(
             Accepted for parity with :meth:`cleanup_old_versions`; no deletes are
             issued by explain.
 
+        versions: list[int], optional
+            Explain cleanup only for the specified dataset versions.
+
         include_files: bool, default False
             If `True`, include candidate files in the explanation up to
             ``max_files`` entries. Aggregate stats always include all candidates.
@@ -3243,7 +3254,7 @@ def explain_cleanup_old_versions(
             Maximum number of candidate files to include when ``include_files``
             is `True`.
         """
-        if older_than is None and retain_versions is None:
+        if older_than is None and retain_versions is None and versions is None:
             older_than = timedelta(days=14)
         if max_files <= 0:
             raise ValueError("max_files must be positive")
@@ -3254,6 +3265,7 @@ def explain_cleanup_old_versions(
             delete_unverified,
             error_if_tagged_old_versions,
             delete_rate_limit,
+            versions,
             include_files,
             max_files,
         )
diff --git a/python/python/tests/test_dataset.py b/python/python/tests/test_dataset.py
index ae49b8cab3d..6093ff2ce38 100644
--- a/python/python/tests/test_dataset.py
+++ b/python/python/tests/test_dataset.py
@@ -1734,6 +1734,24 @@ def test_cleanup_with_retain_versions(tmp_path: Path):
     assert ds.count_rows() == len(ds.to_table())
 
 
+def test_cleanup_specific_versions(tmp_path: Path):
+    base_dir = tmp_path / "cleanup_specific_versions"
+    table = pa.Table.from_pydict({"a": range(100), "b": range(100)})
+    lance.write_dataset(table, base_dir, mode="create")
+    time.sleep(0.05)
+    lance.write_dataset(table, base_dir, mode="overwrite")
+    time.sleep(0.05)
+    lance.write_dataset(table, base_dir, mode="overwrite")
+    time.sleep(0.05)
+    ds = lance.write_dataset(table, base_dir, mode="append")
+
+    assert [v["version"] for v in ds.versions()] == [1, 2, 3, 4]
+
+    stats = ds.cleanup_old_versions(versions=[2])
+    assert stats.old_versions == 1
+    assert [v["version"] for v in ds.versions()] == [1, 3, 4]
+
+
 def test_cleanup_with_older_than_and_retain_versions(tmp_path: Path):
     base_dir = tmp_path / "cleanup_policy"
     table = pa.Table.from_pydict({"a": range(100), "b": range(100)})
diff --git a/python/src/dataset.rs b/python/src/dataset.rs
index 1191309a1f7..bd243fade58 100644
--- a/python/src/dataset.rs
+++ b/python/src/dataset.rs
@@ -796,6 +796,7 @@ impl Dataset {
         delete_unverified: Option<bool>,
         error_if_tagged_old_versions: Option<bool>,
         delete_rate_limit: Option<u64>,
+        versions: Option<Vec<u64>>,
     ) -> lance_core::Result<lance::dataset::cleanup::CleanupPolicy> {
         let mut builder = CleanupPolicyBuilder::default();
         if let Some(v) = older_than_micros {
@@ -814,6 +815,9 @@ impl Dataset {
         if let Some(v) = delete_rate_limit {
             builder = builder.delete_rate_limit(v)?;
         }
+        if let Some(v) = versions {
+            builder = builder.versions(v)?;
+        }
         Ok(builder.build())
     }
 }
@@ -2147,7 +2151,7 @@ impl Dataset {
     }
 
     /// Cleanup old versions from the dataset
-    #[pyo3(signature = (older_than_micros = None, retain_versions = None, delete_unverified = None, error_if_tagged_old_versions = None, delete_rate_limit = None))]
+    #[pyo3(signature = (older_than_micros = None, retain_versions = None, delete_unverified = None, error_if_tagged_old_versions = None, delete_rate_limit = None, versions = None))]
     fn cleanup_old_versions(
         &self,
         older_than_micros: Option<i64>,
@@ -2155,6 +2159,7 @@ impl Dataset {
         delete_unverified: Option<bool>,
         error_if_tagged_old_versions: Option<bool>,
         delete_rate_limit: Option<u64>,
+        versions: Option<Vec<u64>>,
     ) -> PyResult<CleanupStats> {
         let stats = rt()
             .block_on(None, async {
@@ -2165,6 +2170,7 @@ impl Dataset {
                         delete_unverified,
                         error_if_tagged_old_versions,
                         delete_rate_limit,
+                        versions,
                     )
                     .await?;
                 self.ds.cleanup_with_policy(policy).await
@@ -2175,7 +2181,7 @@ impl Dataset {
 
     /// Explain cleanup old versions from the dataset without deleting files
     #[allow(clippy::too_many_arguments)]
-    #[pyo3(signature = (older_than_micros = None, retain_versions = None, delete_unverified = None, error_if_tagged_old_versions = None, delete_rate_limit = None, include_files = false, max_files = 1000))]
+    #[pyo3(signature = (older_than_micros = None, retain_versions = None, delete_unverified = None, error_if_tagged_old_versions = None, delete_rate_limit = None, versions = None, include_files = false, max_files = 1000))]
     fn explain_cleanup_old_versions(
         &self,
         older_than_micros: Option<i64>,
@@ -2183,6 +2189,7 @@ impl Dataset {
         delete_unverified: Option<bool>,
         error_if_tagged_old_versions: Option<bool>,
         delete_rate_limit: Option<u64>,
+        versions: Option<Vec<u64>>,
         include_files: bool,
         max_files: usize,
     ) -> PyResult<CleanupExplanation> {
@@ -2195,6 +2202,7 @@ impl Dataset {
                         delete_unverified,
                         error_if_tagged_old_versions,
                         delete_rate_limit,
+                        versions,
                     )
                     .await?;
                 self.ds
diff --git a/rust/lance/src/dataset/cleanup.rs b/rust/lance/src/dataset/cleanup.rs
index 36ede66bc28..a8ff7ae477b 100644
--- a/rust/lance/src/dataset/cleanup.rs
+++ b/rust/lance/src/dataset/cleanup.rs
@@ -1289,6 +1289,8 @@ pub struct CleanupPolicy {
     pub before_timestamp: Option<DateTime<Utc>>,
     /// If not none, cleanup all versions before the specified version.
     pub before_version: Option<u64>,
+    /// If not none, cleanup only the specified versions.
+    pub versions: Option<HashSet<u64>>,
     /// If true, delete unverified data files even if they are recent
     pub delete_unverified: bool,
     /// If true, return an Error if a tagged version is old
@@ -1312,6 +1314,9 @@ impl CleanupPolicy {
         if let Some(before_version) = self.before_version {
             should_clean &= manifest.version < before_version;
         }
+        if let Some(versions) = self.versions.as_ref() {
+            should_clean &= versions.contains(&manifest.version);
+        }
         should_clean
     }
 }
@@ -1321,6 +1326,7 @@ impl Default for CleanupPolicy {
         Self {
             before_timestamp: None,
             before_version: None,
+            versions: None,
             delete_unverified: false,
             error_if_tagged_old_versions: true,
             clean_referenced_branches: false,
@@ -1347,6 +1353,24 @@ impl CleanupPolicyBuilder {
         self
     }
 
+    /// Cleanup only the specified dataset versions.
+    ///
+    /// This is an exact-version filter. If other policy filters are also
+    /// configured, a manifest is removed only when it satisfies all of them.
+    ///
+    /// # Errors
+    ///
+    /// Returns an error if `versions` is empty.
+    pub fn versions(mut self, versions: Vec<u64>) -> Result<Self> {
+        if versions.is_empty() {
+            return Err(Error::invalid_input(
+                "versions must not be empty when specified",
+            ));
+        }
+        self.policy.versions = Some(versions.into_iter().collect());
+        Ok(self)
+    }
+
     /// Cleanup all versions except the last `n` versions of the dataset.
     ///
     /// # Errors
@@ -3472,6 +3496,37 @@ mod tests {
         );
     }
 
+    #[tokio::test]
+    async fn cleanup_specific_versions_only() {
+        let fixture = MockDatasetFixture::try_new().unwrap();
+        fixture.create_some_data().await.unwrap();
+        fixture.overwrite_some_data().await.unwrap();
+        fixture.overwrite_some_data().await.unwrap();
+
+        let before_count = fixture.count_files().await.unwrap();
+        assert_eq!(before_count.num_manifest_files, 3);
+
+        let policy = CleanupPolicyBuilder::default()
+            .versions(vec![2])
+            .unwrap()
+            .build();
+        let removed = fixture.run_cleanup_with_policy(policy).await.unwrap();
+
+        assert_eq!(removed.old_versions, 1);
+
+        let versions = fixture
+            .open()
+            .await
+            .unwrap()
+            .version_refs()
+            .await
+            .unwrap()
+            .iter()
+            .map(|version| version.version)
+            .collect::<Vec<_>>();
+        assert_eq!(versions, vec![1, 3]);
+    }
+
     #[tokio::test]
     async fn cleanup_before_ts_and_retain_n_recent_versions() {
         let fixture = MockDatasetFixture::try_new().unwrap();