diff --git a/pandas/core/indexes/base.py b/pandas/core/indexes/base.py
index d025734e8d41d..802fd0feedb48 100644
--- a/pandas/core/indexes/base.py
+++ b/pandas/core/indexes/base.py
@@ -3127,7 +3127,8 @@ def _intersection_via_get_indexer(self, other: Index, sort) -> ArrayLike:
         left_unique = self.drop_duplicates()
         right_unique = other.drop_duplicates()
 
-        indexer = left_unique.get_indexer(right_unique)
+        # even though we are unique, we need get_indexer_for for IntervalIndex
+        indexer = left_unique.get_indexer_for(right_unique)
 
         mask = indexer != -1