diff --git a/doc/source/whatsnew/v1.2.0.rst b/doc/source/whatsnew/v1.2.0.rst
index e2521cedb64cc..372dfa0f8ad42 100644
--- a/doc/source/whatsnew/v1.2.0.rst
+++ b/doc/source/whatsnew/v1.2.0.rst
@@ -859,7 +859,7 @@ Other
 - Bug in :meth:`RangeIndex.difference` returning :class:`Int64Index` in some cases where it should return :class:`RangeIndex` (:issue:`38028`)
 - Fixed bug in :func:`assert_series_equal` when comparing a datetime-like array with an equivalent non extension dtype array (:issue:`37609`)
 - Bug in :func:`.is_bool_dtype` would raise when passed a valid string such as ``"boolean"`` (:issue:`38386`)
-
+- Fixed regression in logical operators raising ``ValueError`` when columns of :class:`DataFrame` are a :class:`CategoricalIndex` with unused categories (:issue:`38367`)
 
 .. ---------------------------------------------------------------------------
 
diff --git a/pandas/core/ops/__init__.py b/pandas/core/ops/__init__.py
index d8b5dba424cbf..7b14a5c636abe 100644
--- a/pandas/core/ops/__init__.py
+++ b/pandas/core/ops/__init__.py
@@ -309,11 +309,11 @@ def should_reindex_frame_op(
 
     if fill_value is None and level is None and axis is default_axis:
         # TODO: any other cases we should handle here?
-        cols = left.columns.intersection(right.columns)
 
         # Intersection is always unique so we have to check the unique columns
         left_uniques = left.columns.unique()
         right_uniques = right.columns.unique()
+        cols = left_uniques.intersection(right_uniques)
         if len(cols) and not (cols.equals(left_uniques) and cols.equals(right_uniques)):
             # TODO: is there a shortcut available when len(cols) == 0?
             return True
diff --git a/pandas/tests/frame/test_logical_ops.py b/pandas/tests/frame/test_logical_ops.py
index efabc666993ee..dca12c632a418 100644
--- a/pandas/tests/frame/test_logical_ops.py
+++ b/pandas/tests/frame/test_logical_ops.py
@@ -4,7 +4,7 @@
 import numpy as np
 import pytest
 
-from pandas import DataFrame, Series
+from pandas import CategoricalIndex, DataFrame, Interval, Series, isnull
 import pandas._testing as tm
 
 
@@ -162,3 +162,24 @@ def test_logical_with_nas(self):
         result = d["a"].fillna(False, downcast=False) | d["b"]
         expected = Series([True, True])
         tm.assert_series_equal(result, expected)
+
+    def test_logical_ops_categorical_columns(self):
+        # GH#38367
+        intervals = [Interval(1, 2), Interval(3, 4)]
+        data = DataFrame(
+            [[1, np.nan], [2, np.nan]],
+            columns=CategoricalIndex(
+                intervals, categories=intervals + [Interval(5, 6)]
+            ),
+        )
+        mask = DataFrame(
+            [[False, False], [False, False]], columns=data.columns, dtype=bool
+        )
+        result = mask | isnull(data)
+        expected = DataFrame(
+            [[False, True], [False, True]],
+            columns=CategoricalIndex(
+                intervals, categories=intervals + [Interval(5, 6)]
+            ),
+        )
+        tm.assert_frame_equal(result, expected)