diff --git a/newsfragments/4789.misc.rst b/newsfragments/4789.misc.rst
new file mode 100644
index 0000000000..7f8dfd6a7f
--- /dev/null
+++ b/newsfragments/4789.misc.rst
@@ -0,0 +1 @@
+Don't emit ``Package would be ignored`` warning for explicitly included data files.
diff --git a/setuptools/command/build_py.py b/setuptools/command/build_py.py
index e7d60c6440..7d19330cb4 100644
--- a/setuptools/command/build_py.py
+++ b/setuptools/command/build_py.py
@@ -194,6 +194,10 @@ def analyze_manifest(self) -> None:
             files = ei_cmd.filelist.files
 
         check = _IncludePackageDataAbuse()
+        data_files = {
+            package: filenames
+            for package, _, _, filenames in self.get_data_files_without_manifest()
+        }
         for path in self._filter_build_files(files, egg_info_dir):
             d, f = os.path.split(assert_relative(path))
             prev = None
@@ -208,7 +212,7 @@ def analyze_manifest(self) -> None:
                         continue  # it's a module, not data
                 else:
                     importable = check.importable_subpackage(src_dirs[d], f)
-                    if importable:
+                    if importable and f not in data_files.get(d, {}):
                         check.warn(importable)
                 self.manifest_files.setdefault(src_dirs[d], []).append(path)