diff --git a/changelog.d/3723.change.rst b/changelog.d/3723.change.rst
new file mode 100644
index 0000000000..2ddd02f602
--- /dev/null
+++ b/changelog.d/3723.change.rst
@@ -0,0 +1,2 @@
+Updated ``CCompiler.has_function`` to work with more C99 compilers.
+Deprecated the ```includes`` and ``include_dirs`` keyword arguments.
diff --git a/setuptools/_distutils/ccompiler.py b/setuptools/_distutils/ccompiler.py
index 646353111f..989feded0a 100644
--- a/setuptools/_distutils/ccompiler.py
+++ b/setuptools/_distutils/ccompiler.py
@@ -6,6 +6,7 @@
 import sys
 import os
 import re
+import warnings
 
 from .errors import (
     CompileError,
@@ -824,9 +825,19 @@ def has_function(  # noqa: C901
         libraries=None,
         library_dirs=None,
     ):
-        """Return a boolean indicating whether funcname is supported on
-        the current platform.  The optional arguments can be used to
-        augment the compilation environment.
+        """Return a boolean indicating whether funcname is provided as
+        a symbol on the current platform.  The optional arguments can
+        be used to augment the compilation environment.
+
+        The libraries argument is a list of flags to be passed to the
+        linker to make additional symbol definitions available for
+        linking.
+
+        The includes and include_dirs arguments are deprecated.
+        Usually, supplying include files with function declarations
+        will cause function detection to fail even in cases where the
+        symbol is available for linking.
+
         """
         # this can't be included at module scope because it tries to
         # import math which might not be available at that point - maybe
@@ -835,8 +846,12 @@ def has_function(  # noqa: C901
 
         if includes is None:
             includes = []
+        else:
+            warnings.warn("The include argument is deprecated")
         if include_dirs is None:
             include_dirs = []
+        else:
+            warnings.warn("The include_dirs argument is deprecated")
         if libraries is None:
             libraries = []
         if library_dirs is None:
@@ -845,7 +860,23 @@ def has_function(  # noqa: C901
         f = os.fdopen(fd, "w")
         try:
             for incl in includes:
-                f.write("""#include "%s"\n""" % incl)
+                f.write("""#include %s\n""" % incl)
+            if not includes:
+                # Use "char func(void);" as the prototype to follow
+                # what autoconf does.  This prototype does not match
+                # any well-known function the compiler might recognize
+                # as a builtin, so this ends up as a true link test.
+                # Without a fake prototype, the test would need to
+                # know the exact argument types, and the has_function
+                # interface does not provide that level of information.
+                f.write("""\
+#ifdef __cplusplus
+extern "C"
+#endif
+char %s(void);
+"""
+                    % funcname
+                )
             f.write(
                 """\
 int main (int argc, char **argv) {
diff --git a/setuptools/_distutils/tests/test_unixccompiler.py b/setuptools/_distutils/tests/test_unixccompiler.py
index 3978c23952..afcac0178d 100644
--- a/setuptools/_distutils/tests/test_unixccompiler.py
+++ b/setuptools/_distutils/tests/test_unixccompiler.py
@@ -304,3 +304,19 @@ def test_has_function(self):
         self.cc.output_dir = 'scratch'
         os.chdir(self.mkdtemp())
         self.cc.has_function('abort', includes=['stdlib.h'])
+
+    def test_has_function_prototype(self):
+        # Issue https://github.com/pypa/setuptools/issues/3648
+        # Test prototype-generating behavior.
+
+        # Every C implementation should have these.
+        assert self.cc.has_function('abort')
+        assert self.cc.has_function('exit')
+        # abort() is a valid expression with the <stdlib.h> prototype.
+        assert self.cc.has_function('abort', includes=['<stdlib.h>'])
+        # But exit() is not valid with the actual prototype in scope.
+        assert not self.cc.has_function('exit', includes=['<stdlib.h>'])
+        # And setuptools_does_not_exist is not declared or defined at all.
+        assert not self.cc.has_function('setuptools_does_not_exist')
+        assert not self.cc.has_function('setuptools_does_not_exist',
+                                        includes=['<stdio.h>'])