diff --git a/doc/source/whatsnew/v2.0.0.rst b/doc/source/whatsnew/v2.0.0.rst
index cbad169fe4d56..6a765094c551f 100644
--- a/doc/source/whatsnew/v2.0.0.rst
+++ b/doc/source/whatsnew/v2.0.0.rst
@@ -831,6 +831,7 @@ Interval
 
 Indexing
 ^^^^^^^^
+- Bug in :meth:`DataFrame.__setitem__` raising when indexer is a :class:`DataFrame` with ``boolean`` dtype (:issue:`47125`)
 - Bug in :meth:`DataFrame.reindex` filling with wrong values when indexing columns and index for ``uint`` dtypes (:issue:`48184`)
 - Bug in :meth:`DataFrame.loc` coercing dtypes when setting values with a list indexer (:issue:`49159`)
 - Bug in :meth:`DataFrame.loc` raising ``ValueError`` with ``bool`` indexer and :class:`MultiIndex` (:issue:`47687`)
diff --git a/pandas/core/frame.py b/pandas/core/frame.py
index 798ea8a61093a..728e41e6c1d3a 100644
--- a/pandas/core/frame.py
+++ b/pandas/core/frame.py
@@ -4087,7 +4087,7 @@ def _setitem_frame(self, key, value):
                 raise ValueError("Array conditional must be same shape as self")
             key = self._constructor(key, **self._construct_axes_dict())
 
-        if key.size and not is_bool_dtype(key.values):
+        if key.size and not all(is_bool_dtype(dtype) for dtype in key.dtypes):
             raise TypeError(
                 "Must pass DataFrame or 2-d ndarray with boolean values only"
             )
diff --git a/pandas/tests/frame/indexing/test_setitem.py b/pandas/tests/frame/indexing/test_setitem.py
index e27f9fe9995ad..cb0798ffb601a 100644
--- a/pandas/tests/frame/indexing/test_setitem.py
+++ b/pandas/tests/frame/indexing/test_setitem.py
@@ -1125,6 +1125,19 @@ def test_loc_setitem_all_false_boolean_two_blocks(self):
         df.loc[indexer, ["b"]] = DataFrame({"b": [5, 6]}, index=[0, 1])
         tm.assert_frame_equal(df, expected)
 
+    def test_setitem_ea_boolean_mask(self):
+        # GH#47125
+        df = DataFrame([[-1, 2], [3, -4]])
+        expected = DataFrame([[0, 2], [3, 0]])
+        boolean_indexer = DataFrame(
+            {
+                0: Series([True, False], dtype="boolean"),
+                1: Series([pd.NA, True], dtype="boolean"),
+            }
+        )
+        df[boolean_indexer] = 0
+        tm.assert_frame_equal(df, expected)
+
 
 class TestDataFrameSetitemCopyViewSemantics:
     def test_setitem_always_copy(self, float_frame):