diff --git a/newsfragments/4559.misc.rst b/newsfragments/4559.misc.rst
new file mode 100644
index 0000000000..34b5a30664
--- /dev/null
+++ b/newsfragments/4559.misc.rst
@@ -0,0 +1,2 @@
+Prevent deprecation warning from ``pypa/wheel#631`` to accidentally
+trigger when validating ``pyproject.toml``.
diff --git a/setuptools/config/_apply_pyprojecttoml.py b/setuptools/config/_apply_pyprojecttoml.py
index 8224a02631..7b9c0b1a59 100644
--- a/setuptools/config/_apply_pyprojecttoml.py
+++ b/setuptools/config/_apply_pyprojecttoml.py
@@ -276,6 +276,11 @@ def _valid_command_options(cmdclass: Mapping = EMPTY) -> dict[str, set[str]]:
 
 
 def _load_ep(ep: metadata.EntryPoint) -> tuple[str, type] | None:
+    if ep.value.startswith("wheel.bdist_wheel"):
+        # Ignore deprecated entrypoint from wheel and avoid warning pypa/wheel#631
+        # TODO: remove check when `bdist_wheel` has been fully removed from pypa/wheel
+        return None
+
     # Ignore all the errors
     try:
         return (ep.name, ep.load())