diff --git a/doc/source/whatsnew/v3.0.0.rst b/doc/source/whatsnew/v3.0.0.rst
index 7ec50137c3039..f929c63c6bf82 100644
--- a/doc/source/whatsnew/v3.0.0.rst
+++ b/doc/source/whatsnew/v3.0.0.rst
@@ -641,6 +641,7 @@ Other Deprecations
 - Deprecated strings ``w``, ``d``, ``MIN``, ``MS``, ``US`` and ``NS`` denoting units in :class:`Timedelta` in favour of ``W``, ``D``, ``min``, ``ms``, ``us`` and ``ns`` (:issue:`59051`)
 - Deprecated the ``arg`` parameter of ``Series.map``; pass the added ``func`` argument instead. (:issue:`61260`)
 - Deprecated using ``epoch`` date format in :meth:`DataFrame.to_json` and :meth:`Series.to_json`, use ``iso`` instead. (:issue:`57063`)
+- Deprecated allowing ``fill_value`` that cannot be held in the original dtype (excepting NA values for integer and bool dtypes) in :meth:`Series.unstack` and :meth:`DataFrame.unstack` (:issue:`12189`, :issue:`53868`)
 
 .. ---------------------------------------------------------------------------
 .. _whatsnew_300.prior_deprecations:
diff --git a/pandas/core/reshape/reshape.py b/pandas/core/reshape/reshape.py
index dd22f900be926..e101944e72ef0 100644
--- a/pandas/core/reshape/reshape.py
+++ b/pandas/core/reshape/reshape.py
@@ -13,7 +13,10 @@
 from pandas._config.config import get_option
 
 import pandas._libs.reshape as libreshape
-from pandas.errors import PerformanceWarning
+from pandas.errors import (
+    Pandas4Warning,
+    PerformanceWarning,
+)
 from pandas.util._decorators import cache_readonly
 from pandas.util._exceptions import find_stack_level
 
@@ -28,7 +31,10 @@
     needs_i8_conversion,
 )
 from pandas.core.dtypes.dtypes import ExtensionDtype
-from pandas.core.dtypes.missing import notna
+from pandas.core.dtypes.missing import (
+    isna,
+    notna,
+)
 
 import pandas.core.algorithms as algos
 from pandas.core.algorithms import (
@@ -298,7 +304,25 @@ def get_new_values(self, values, fill_value=None):
                 new_values[:] = fill_value
         else:
             if not mask_all:
+                old_dtype = dtype
                 dtype, fill_value = maybe_promote(dtype, fill_value)
+                if old_dtype != dtype:
+                    if old_dtype.kind not in "iub":
+                        warnings.warn(
+                            # GH#12189, GH#53868
+                            "Using a fill_value that cannot be held in the existing "
+                            "dtype is deprecated and will raise in a future version.",
+                            Pandas4Warning,
+                            stacklevel=find_stack_level(),
+                        )
+                    elif not isna(fill_value):
+                        warnings.warn(
+                            # GH#12189, GH#53868
+                            "Using a fill_value that cannot be held in the existing "
+                            "dtype is deprecated and will raise in a future version.",
+                            Pandas4Warning,
+                            stacklevel=find_stack_level(),
+                        )
             new_values = np.empty(result_shape, dtype=dtype)
             if not mask_all:
                 new_values.fill(fill_value)
diff --git a/pandas/tests/frame/test_stack_unstack.py b/pandas/tests/frame/test_stack_unstack.py
index 756d454ebd11f..9124443219e3c 100644
--- a/pandas/tests/frame/test_stack_unstack.py
+++ b/pandas/tests/frame/test_stack_unstack.py
@@ -105,8 +105,12 @@ def test_unstack_fill(self, future_stack):
         )
         tm.assert_frame_equal(result, expected)
 
-        # From a series with incorrect data type for fill_value
-        result = data.unstack(fill_value=0.5)
+        msg = (
+            "Using a fill_value that cannot be held in the existing dtype is deprecated"
+        )
+        with tm.assert_produces_warning(Pandas4Warning, match=msg):
+            # From a series with incorrect data type for fill_value
+            result = data.unstack(fill_value=0.5)
         expected = DataFrame(
             {"a": [1, 0.5, 5], "b": [2, 4, 0.5]}, index=["x", "y", "z"], dtype=float
         )
@@ -161,8 +165,12 @@ def test_unstack_fill_frame(self):
         expected["B"] = expected["B"].astype(np.float64)
         tm.assert_frame_equal(result, expected)
 
-        # From a dataframe with incorrect data type for fill_value
-        result = df.unstack(fill_value=0.5)
+        msg = (
+            "Using a fill_value that cannot be held in the existing dtype is deprecated"
+        )
+        with tm.assert_produces_warning(Pandas4Warning, match=msg):
+            # From a dataframe with incorrect data type for fill_value
+            result = df.unstack(fill_value=0.5)
 
         rows = [[1, 3, 2, 4], [0.5, 5, 0.5, 6], [7, 0.5, 8, 0.5]]
         expected = DataFrame(rows, index=list("xyz"), dtype=float)