diff --git a/doc/whats_new/v1.4.rst b/doc/whats_new/v1.4.rst
index 8dbd867b0c9ba..c56e67024a890 100644
--- a/doc/whats_new/v1.4.rst
+++ b/doc/whats_new/v1.4.rst
@@ -250,6 +250,13 @@ Changelog
 - |Enhancement| Added `neg_root_mean_squared_log_error_scorer` as scorer
   :pr:`26734` by :user:`Alejandro Martin Gil <101AlexMartin>`.
 
+:mod:`sklearn.preprocessing`
+............................
+
+- |Enhancement| Improves warnings in :class:`preprocessing.FunctionTransfomer` when
+  `func` returns a pandas dataframe and the output is configured to be pandas.
+  :pr:`26944` by `Thomas Fan`_.
+
 :mod:`sklearn.model_selection`
 ..............................
 
diff --git a/sklearn/preprocessing/_function_transformer.py b/sklearn/preprocessing/_function_transformer.py
index f1df0f43dc96e..fa755265d7bc2 100644
--- a/sklearn/preprocessing/_function_transformer.py
+++ b/sklearn/preprocessing/_function_transformer.py
@@ -4,10 +4,12 @@
 
 from ..base import BaseEstimator, TransformerMixin, _fit_context
 from ..utils._param_validation import StrOptions
+from ..utils._set_output import _get_output_config
 from ..utils.metaestimators import available_if
 from ..utils.validation import (
     _allclose_dense_sparse,
     _check_feature_names_in,
+    _is_pandas_df,
     check_array,
 )
 
@@ -237,7 +239,20 @@ def transform(self, X):
             Transformed input.
         """
         X = self._check_input(X, reset=False)
-        return self._transform(X, func=self.func, kw_args=self.kw_args)
+        out = self._transform(X, func=self.func, kw_args=self.kw_args)
+
+        output_config = _get_output_config("transform", self)["dense"]
+        if (
+            output_config == "pandas"
+            and self.feature_names_out is None
+            and not _is_pandas_df(out)
+        ):
+            warnings.warn(
+                "When `set_output` is configured to be 'pandas', `func` should return "
+                "a DataFrame to follow the `set_output` API  or `feature_names_out` "
+                "should be defined."
+            )
+        return out
 
     def inverse_transform(self, X):
         """Transform X using the inverse function.
@@ -338,13 +353,8 @@ def set_output(self, *, transform=None):
         self : estimator instance
             Estimator instance.
         """
-        if hasattr(super(), "set_output"):
-            return super().set_output(transform=transform)
-
-        if transform == "pandas" and self.feature_names_out is None:
-            warnings.warn(
-                'With transform="pandas", `func` should return a DataFrame to follow'
-                " the set_output API."
-            )
+        if not hasattr(self, "_sklearn_output_config"):
+            self._sklearn_output_config = {}
 
+        self._sklearn_output_config["transform"] = transform
         return self
diff --git a/sklearn/preprocessing/tests/test_function_transformer.py b/sklearn/preprocessing/tests/test_function_transformer.py
index d843f56002619..c4b2f79f288f0 100644
--- a/sklearn/preprocessing/tests/test_function_transformer.py
+++ b/sklearn/preprocessing/tests/test_function_transformer.py
@@ -451,13 +451,26 @@ def test_set_output_func():
     assert isinstance(X_trans, pd.DataFrame)
     assert_array_equal(X_trans.columns, ["a", "b"])
 
-    # If feature_names_out is not defined, then a warning is raised in
-    # `set_output`
     ft = FunctionTransformer(lambda x: 2 * x)
-    msg = "should return a DataFrame to follow the set_output API"
-    with pytest.warns(UserWarning, match=msg):
-        ft.set_output(transform="pandas")
+    ft.set_output(transform="pandas")
 
-    X_trans = ft.fit_transform(X)
+    # no warning is raised when func returns a panda dataframe
+    with warnings.catch_warnings():
+        warnings.simplefilter("error", UserWarning)
+        X_trans = ft.fit_transform(X)
     assert isinstance(X_trans, pd.DataFrame)
     assert_array_equal(X_trans.columns, ["a", "b"])
+
+    # Warning is raised when func returns a ndarray
+    ft_np = FunctionTransformer(lambda x: np.asarray(x))
+    ft_np.set_output(transform="pandas")
+
+    msg = "When `set_output` is configured to be 'pandas'"
+    with pytest.warns(UserWarning, match=msg):
+        ft_np.fit_transform(X)
+
+    # default transform does not warn
+    ft_np.set_output(transform="default")
+    with warnings.catch_warnings():
+        warnings.simplefilter("error", UserWarning)
+        ft_np.fit_transform(X)