diff --git a/clang-tools-extra/test/clang-tidy/checkers/Inputs/portability-restrict-system-includes/a.h b/clang-tools-extra/test/clang-tidy/checkers/Inputs/portability-restrict-system-includes/system/float.h
rename from clang-tools-extra/test/clang-tidy/checkers/Inputs/portability-restrict-system-includes/a.h
rename to clang-tools-extra/test/clang-tidy/checkers/Inputs/portability-restrict-system-includes/system/float.h
diff --git a/clang-tools-extra/test/clang-tidy/checkers/Inputs/portability-restrict-system-includes/system/j.h b/clang-tools-extra/test/clang-tidy/checkers/Inputs/portability-restrict-system-includes/system/j.h
deleted file mode 100644
diff --git a/clang-tools-extra/test/clang-tidy/checkers/Inputs/portability-restrict-system-includes/system/cstdarg.h b/clang-tools-extra/test/clang-tidy/checkers/Inputs/portability-restrict-system-includes/system/stddef.h
rename from clang-tools-extra/test/clang-tidy/checkers/Inputs/portability-restrict-system-includes/system/cstdarg.h
rename to clang-tools-extra/test/clang-tidy/checkers/Inputs/portability-restrict-system-includes/system/stddef.h
diff --git a/clang-tools-extra/test/clang-tidy/checkers/Inputs/portability-restrict-system-includes/system/cstdlib.h b/clang-tools-extra/test/clang-tidy/checkers/Inputs/portability-restrict-system-includes/system/stdint.h
rename from clang-tools-extra/test/clang-tidy/checkers/Inputs/portability-restrict-system-includes/system/cstdlib.h
rename to clang-tools-extra/test/clang-tidy/checkers/Inputs/portability-restrict-system-includes/system/stdint.h
diff --git a/clang-tools-extra/test/clang-tidy/checkers/portability-restrict-system-includes-allow.cpp b/clang-tools-extra/test/clang-tidy/checkers/portability-restrict-system-includes-allow.cpp
--- a/clang-tools-extra/test/clang-tidy/checkers/portability-restrict-system-includes-allow.cpp
+++ b/clang-tools-extra/test/clang-tidy/checkers/portability-restrict-system-includes-allow.cpp
@@ -1,5 +1,6 @@
 // RUN: %check_clang_tidy %s portability-restrict-system-includes %t \
-// RUN:     -- -config="{CheckOptions: [{key: portability-restrict-system-includes.Includes, value: '*,-stddef.h'}]}"
+// RUN:     -- -config="{CheckOptions: [{key: portability-restrict-system-includes.Includes, value: '*,-stddef.h'}]}" \
+// RUN:     -- -isystem %S/Inputs/portability-restrict-system-includes/system
 
 // Test block-list functionality: allow all but stddef.h.
 
diff --git a/clang-tools-extra/test/clang-tidy/checkers/portability-restrict-system-includes-disallow.cpp b/clang-tools-extra/test/clang-tidy/checkers/portability-restrict-system-includes-disallow.cpp
--- a/clang-tools-extra/test/clang-tidy/checkers/portability-restrict-system-includes-disallow.cpp
+++ b/clang-tools-extra/test/clang-tidy/checkers/portability-restrict-system-includes-disallow.cpp
@@ -1,5 +1,6 @@
 // RUN: %check_clang_tidy %s portability-restrict-system-includes %t \
-// RUN:     -- -config="{CheckOptions: [{key: portability-restrict-system-includes.Includes, value: '-*,stddef.h'}]}"
+// RUN:     -- -config="{CheckOptions: [{key: portability-restrict-system-includes.Includes, value: '-*,stddef.h'}]}" \
+// RUN:     -- -isystem %S/Inputs/portability-restrict-system-includes/system
 
 // Test allow-list functionality: disallow all but stddef.h.
 
diff --git a/clang-tools-extra/test/clang-tidy/checkers/portability-restrict-system-includes-glob.cpp b/clang-tools-extra/test/clang-tidy/checkers/portability-restrict-system-includes-glob.cpp
--- a/clang-tools-extra/test/clang-tidy/checkers/portability-restrict-system-includes-glob.cpp
+++ b/clang-tools-extra/test/clang-tidy/checkers/portability-restrict-system-includes-glob.cpp
@@ -1,5 +1,6 @@
 // RUN: %check_clang_tidy %s portability-restrict-system-includes %t \
-// RUN:     -- -config="{CheckOptions: [{key: portability-restrict-system-includes.Includes, value: '-*,std*.h'}]}"
+// RUN:     -- -config="{CheckOptions: [{key: portability-restrict-system-includes.Includes, value: '-*,std*.h'}]}" \
+// RUN:     -- -isystem %S/Inputs/portability-restrict-system-includes/system
 
 // Test glob functionality: disallow all headers except those that match
 // pattern "std*.h".