diff --git a/doc/source/whatsnew/v1.3.0.rst b/doc/source/whatsnew/v1.3.0.rst
index 2b0b62ab7facf..8ebb5437978ea 100644
--- a/doc/source/whatsnew/v1.3.0.rst
+++ b/doc/source/whatsnew/v1.3.0.rst
@@ -830,7 +830,7 @@ ExtensionArray
 - Bug in :meth:`DataFrame.where` when ``other`` is a :class:`Series` with :class:`ExtensionArray` dtype (:issue:`38729`)
 - Fixed bug where :meth:`Series.idxmax`, :meth:`Series.idxmin` and ``argmax/min`` fail when the underlying data is :class:`ExtensionArray` (:issue:`32749`, :issue:`33719`, :issue:`36566`)
 - Fixed a bug where some properties of subclasses of :class:`PandasExtensionDtype` where improperly cached (:issue:`40329`)
--
+- Bug in :meth:`DataFrame.mask` where masking a :class:`Dataframe` with an :class:`ExtensionArray` dtype raises ``ValueError`` (:issue:`40941`)
 
 Styler
 ^^^^^^
diff --git a/pandas/core/generic.py b/pandas/core/generic.py
index cbc353eead464..bad42a85aeeee 100644
--- a/pandas/core/generic.py
+++ b/pandas/core/generic.py
@@ -8958,7 +8958,7 @@ def _where(
                     join="left",
                     axis=axis,
                     level=level,
-                    fill_value=np.nan,
+                    fill_value=None,
                     copy=False,
                 )
 
diff --git a/pandas/tests/frame/indexing/test_mask.py b/pandas/tests/frame/indexing/test_mask.py
index afa8c757c23e4..364475428e529 100644
--- a/pandas/tests/frame/indexing/test_mask.py
+++ b/pandas/tests/frame/indexing/test_mask.py
@@ -5,7 +5,10 @@
 import numpy as np
 
 from pandas import (
+    NA,
     DataFrame,
+    Series,
+    StringDtype,
     isna,
 )
 import pandas._testing as tm
@@ -99,3 +102,24 @@ def test_mask_try_cast_deprecated(frame_or_series):
     with tm.assert_produces_warning(FutureWarning):
         # try_cast keyword deprecated
         obj.mask(mask, -1, try_cast=True)
+
+
+def test_mask_stringdtype():
+    # GH 40824
+    df = DataFrame(
+        {"A": ["foo", "bar", "baz", NA]},
+        index=["id1", "id2", "id3", "id4"],
+        dtype=StringDtype(),
+    )
+    filtered_df = DataFrame(
+        {"A": ["this", "that"]}, index=["id2", "id3"], dtype=StringDtype()
+    )
+    filter_ser = Series([False, True, True, False])
+    result = df.mask(filter_ser, filtered_df)
+
+    expected = DataFrame(
+        {"A": [NA, "this", "that", NA]},
+        index=["id1", "id2", "id3", "id4"],
+        dtype=StringDtype(),
+    )
+    tm.assert_frame_equal(result, expected)
diff --git a/pandas/tests/frame/indexing/test_where.py b/pandas/tests/frame/indexing/test_where.py
index 574fa46d10f67..7ffe2fb9ab1ff 100644
--- a/pandas/tests/frame/indexing/test_where.py
+++ b/pandas/tests/frame/indexing/test_where.py
@@ -10,6 +10,7 @@
     DataFrame,
     DatetimeIndex,
     Series,
+    StringDtype,
     Timestamp,
     date_range,
     isna,
@@ -709,3 +710,22 @@ def test_where_copies_with_noop(frame_or_series):
     where_res *= 2
 
     tm.assert_equal(result, expected)
+
+
+def test_where_string_dtype(frame_or_series):
+    # GH40824
+    obj = frame_or_series(
+        ["a", "b", "c", "d"], index=["id1", "id2", "id3", "id4"], dtype=StringDtype()
+    )
+    filtered_obj = frame_or_series(
+        ["b", "c"], index=["id2", "id3"], dtype=StringDtype()
+    )
+    filter_ser = Series([False, True, True, False])
+
+    result = obj.where(filter_ser, filtered_obj)
+    expected = frame_or_series(
+        [pd.NA, "b", "c", pd.NA],
+        index=["id1", "id2", "id3", "id4"],
+        dtype=StringDtype(),
+    )
+    tm.assert_equal(result, expected)
diff --git a/pandas/tests/series/indexing/test_mask.py b/pandas/tests/series/indexing/test_mask.py
index dc4fb530dbb52..a4dda3a5c0c5b 100644
--- a/pandas/tests/series/indexing/test_mask.py
+++ b/pandas/tests/series/indexing/test_mask.py
@@ -1,7 +1,11 @@
 import numpy as np
 import pytest
 
-from pandas import Series
+from pandas import (
+    NA,
+    Series,
+    StringDtype,
+)
 import pandas._testing as tm
 
 
@@ -63,3 +67,22 @@ def test_mask_inplace():
     rs = s.copy()
     rs.mask(cond, -s, inplace=True)
     tm.assert_series_equal(rs, s.mask(cond, -s))
+
+
+def test_mask_stringdtype():
+    # GH 40824
+    ser = Series(
+        ["foo", "bar", "baz", NA],
+        index=["id1", "id2", "id3", "id4"],
+        dtype=StringDtype(),
+    )
+    filtered_ser = Series(["this", "that"], index=["id2", "id3"], dtype=StringDtype())
+    filter_ser = Series([False, True, True, False])
+    result = ser.mask(filter_ser, filtered_ser)
+
+    expected = Series(
+        [NA, "this", "that", NA],
+        index=["id1", "id2", "id3", "id4"],
+        dtype=StringDtype(),
+    )
+    tm.assert_series_equal(result, expected)