diff --git a/doc/source/whatsnew/v3.0.0.rst b/doc/source/whatsnew/v3.0.0.rst
index b4aa6447c0a1b..565cd1c54d42c 100644
--- a/doc/source/whatsnew/v3.0.0.rst
+++ b/doc/source/whatsnew/v3.0.0.rst
@@ -703,6 +703,7 @@ Indexing
 - Bug in :meth:`DataFrame.loc` with inconsistent behavior of loc-set with 2 given indexes to Series (:issue:`59933`)
 - Bug in :meth:`Index.get_indexer` and similar methods when ``NaN`` is located at or after position 128 (:issue:`58924`)
 - Bug in :meth:`MultiIndex.insert` when a new value inserted to a datetime-like level gets cast to ``NaT`` and fails indexing (:issue:`60388`)
+- Bug in :meth:`Series.mask` unexpectedly filling ``pd.NA`` (:issue:`60729`)
 - Bug in printing :attr:`Index.names` and :attr:`MultiIndex.levels` would not escape single quotes (:issue:`60190`)
 - Bug in reindexing of :class:`DataFrame` with :class:`PeriodDtype` columns in case of consolidated block (:issue:`60980`, :issue:`60273`)
 
diff --git a/pandas/core/generic.py b/pandas/core/generic.py
index 0c3f535df9ce2..f0fc8fa4d695f 100644
--- a/pandas/core/generic.py
+++ b/pandas/core/generic.py
@@ -28,6 +28,7 @@
 
 from pandas._libs import lib
 from pandas._libs.lib import is_range_indexer
+from pandas._libs.missing import NA
 from pandas._libs.tslibs import (
     Period,
     Timestamp,
@@ -9701,6 +9702,7 @@ def _where(
         # align the cond to same shape as myself
         cond = common.apply_if_callable(cond, self)
         if isinstance(cond, NDFrame):
+            cond = cond.fillna(True)
             # CoW: Make sure reference is not kept alive
             if cond.ndim == 1 and self.ndim == 2:
                 cond = cond._constructor_expanddim(
@@ -9715,6 +9717,7 @@ def _where(
             if cond.shape != self.shape:
                 raise ValueError("Array conditional must be same shape as self")
             cond = self._constructor(cond, **self._construct_axes_dict(), copy=False)
+            cond = cond.fillna(True)
 
         # make sure we are boolean
         fill_value = bool(inplace)
@@ -10097,6 +10100,16 @@ def mask(
         if not hasattr(cond, "__invert__"):
             cond = np.array(cond)
 
+        if isinstance(cond, np.ndarray):
+            if all(
+                x is NA or isinstance(x, (np.bool_, bool)) or x is np.nan
+                for x in cond.flatten()
+            ):
+                if not cond.flags.writeable:
+                    cond.setflags(write=True)
+                cond[isna(cond)] = False
+                cond = cond.astype(bool)
+
         return self._where(
             ~cond,
             other=other,
diff --git a/pandas/tests/series/indexing/test_mask.py b/pandas/tests/series/indexing/test_mask.py
index 3c21cd0d5ca64..3bfade287bd05 100644
--- a/pandas/tests/series/indexing/test_mask.py
+++ b/pandas/tests/series/indexing/test_mask.py
@@ -1,6 +1,8 @@
 import numpy as np
 import pytest
 
+import pandas.util._test_decorators as td
+
 from pandas import Series
 import pandas._testing as tm
 
@@ -67,3 +69,26 @@ def test_mask_inplace():
     rs = s.copy()
     rs.mask(cond, -s, inplace=True)
     tm.assert_series_equal(rs, s.mask(cond, -s))
+
+
+@pytest.mark.parametrize(
+    "dtype",
+    [
+        "Int64",
+        pytest.param("int64[pyarrow]", marks=td.skip_if_no("pyarrow")),
+    ],
+)
+def test_mask_na(dtype):
+    # We should not be filling pd.NA. See GH#60729
+    series = Series([None, 1, 2, None, 3, 4, None], dtype=dtype)
+    cond = series <= 2
+    expected = Series([None, -99, -99, None, 3, 4, None], dtype=dtype)
+
+    result = series.mask(cond, -99)
+    tm.assert_series_equal(result, expected)
+
+    result = series.mask(cond.to_list(), -99)
+    tm.assert_series_equal(result, expected)
+
+    result = series.mask(cond.to_numpy(), -99)
+    tm.assert_series_equal(result, expected)