diff --git a/pandas/_libs/index.pyx b/pandas/_libs/index.pyx
index 8c30f55e58e14..33fa191abd123 100644
--- a/pandas/_libs/index.pyx
+++ b/pandas/_libs/index.pyx
@@ -272,9 +272,10 @@ cdef class IndexEngine:
         self._ensure_mapping_populated()
         values = np.array(self._get_index_values(), copy=False)
         targets_mask = isnaobj(targets)
+        values_mask = isnaobj(values)
         if targets_mask.any():
             targets[targets_mask] = 0
-            values[isnaobj(values)] = 0
+            values[values_mask] = 0
 
         stargets = set(targets)
         n = len(values)
@@ -325,8 +326,13 @@ cdef class IndexEngine:
                         n_alloc += 10_000
                         result = np.resize(result, n_alloc)
 
-                    result[count] = j
-                    count += 1
+                    if val == 0:
+                        if targets_mask[i] == values_mask[j]:
+                            result[count] = j
+                            count += 1
+                    else:
+                        result[count] = j
+                        count += 1
 
             # value not found
             else: