diff --git a/python/python/lance/dataset.py b/python/python/lance/dataset.py
index 831e194f9f3..3f6b553bf5f 100644
--- a/python/python/lance/dataset.py
+++ b/python/python/lance/dataset.py
@@ -4622,6 +4622,10 @@ def migrate_manifest_paths_v2(self):
         """
         self._ds.migrate_manifest_paths_v2()
 
+    def cleanup_frag_reuse_index(self) -> None:
+        """Prune obsolete generations from the ``__lance_frag_reuse`` system index."""
+        self._ds.cleanup_frag_reuse_index()
+
     def delete_config_keys(self, keys: list[str]) -> None:
         """Delete specified configuration keys from the dataset.
 
diff --git a/python/python/lance/lance/__init__.pyi b/python/python/lance/lance/__init__.pyi
index 38d82738063..9af7167940e 100644
--- a/python/python/lance/lance/__init__.pyi
+++ b/python/python/lance/lance/__init__.pyi
@@ -446,6 +446,7 @@ class _Dataset:
     ) -> Tuple[_Dataset, Transaction]: ...
     def validate(self): ...
     def migrate_manifest_paths_v2(self): ...
+    def cleanup_frag_reuse_index(self) -> None: ...
     def drop_columns(self, columns: List[str]): ...
     def add_columns_from_reader(
         self, reader: pa.RecordBatchReader, batch_size: Optional[int] = None
diff --git a/python/python/tests/test_optimize.py b/python/python/tests/test_optimize.py
index ccd889db116..ec3fbe53431 100644
--- a/python/python/tests/test_optimize.py
+++ b/python/python/tests/test_optimize.py
@@ -324,6 +324,49 @@ def test_defer_index_remap(tmp_path: Path):
     assert any(idx.name == "__lance_frag_reuse" for idx in indices)
 
 
+def test_cleanup_frag_reuse_index(tmp_path: Path):
+    """cleanup_frag_reuse_index prunes all reuse generations that every user
+    index has caught up to.
+
+    Setup: 6 fragments, one BTREE scalar index.  Compact with
+    defer_index_remap=True so the frag-reuse index is populated.  Rebuild the
+    scalar index (create_scalar_index with replace=True) so it is newer than the
+    reuse generation, meaning the generation can be pruned.  Then call
+    cleanup_frag_reuse_index and verify that num_versions drops to 0.
+    """
+    base_dir = tmp_path / "dataset"
+    data = pa.table({"i": range(6_000), "val": range(6_000)})
+    dataset = lance.write_dataset(data, base_dir, max_rows_per_file=1_000)
+    dataset.create_scalar_index("i", "BTREE")
+
+    dataset.delete("i < 500")
+    dataset.optimize.compact_files(
+        target_rows_per_fragment=2_000, defer_index_remap=True, num_threads=1
+    )
+
+    dataset = lance.dataset(base_dir)
+    assert any(
+        idx.name == "__lance_frag_reuse" for idx in dataset.describe_indices()
+    ), "precondition: defer_index_remap must have created the frag-reuse index"
+
+    before_stats = dataset.stats.index_stats("__lance_frag_reuse")
+    assert before_stats["num_versions"] >= 1, (
+        "precondition: frag-reuse index must have at least one version before cleanup"
+    )
+
+    dataset.create_scalar_index("i", "BTREE", replace=True)
+    dataset = lance.dataset(base_dir)
+
+    dataset.cleanup_frag_reuse_index()
+
+    dataset = lance.dataset(base_dir)
+    after_stats = dataset.stats.index_stats("__lance_frag_reuse")
+    assert after_stats["num_versions"] == 0, (
+        f"cleanup_frag_reuse_index should have pruned all reuse generations "
+        f"but num_versions={after_stats['num_versions']}"
+    )
+
+
 @pytest.mark.filterwarnings("ignore::DeprecationWarning")
 def test_describe_indices_matches_list_indices_for_frag_reuse(tmp_path: Path):
     """describe_indices() and list_indices() must agree on the index_type
diff --git a/python/src/dataset.rs b/python/src/dataset.rs
index 8bfa81aeae4..e8e864d300a 100644
--- a/python/src/dataset.rs
+++ b/python/src/dataset.rs
@@ -2788,6 +2788,17 @@ impl Dataset {
         Ok(())
     }
 
+    fn cleanup_frag_reuse_index(&mut self) -> PyResult<()> {
+        let mut new_self = self.ds.as_ref().clone();
+        rt().block_on(
+            None,
+            lance::dataset::index::frag_reuse::cleanup_frag_reuse_index(&mut new_self),
+        )?
+        .map_err(|err: lance::Error| PyIOError::new_err(err.to_string()))?;
+        self.ds = Arc::new(new_self);
+        Ok(())
+    }
+
     fn drop_columns(&mut self, columns: Vec<String>) -> PyResult<()> {
         let mut new_self = self.ds.as_ref().clone();
         let columns: Vec<_> = columns.iter().map(|s| s.as_str()).collect();