diff --git a/_tools/check_mod_exports.ts b/_tools/check_mod_exports.ts
index e33f5f8ff963..ba5cbc1d04bd 100644
--- a/_tools/check_mod_exports.ts
+++ b/_tools/check_mod_exports.ts
@@ -2,6 +2,7 @@
 // Copyright 2018-2026 the Deno authors. MIT license.
 
 import { walk } from "../fs/walk.ts";
+import { basename } from "../path/basename.ts";
 import { relative } from "../path/relative.ts";
 import { dirname } from "../path/dirname.ts";
 import * as colors from "../fmt/colors.ts";
@@ -11,6 +12,28 @@ import { fromFileUrl } from "@std/path/from-file-url";
 
 const FAIL_FAST = Deno.args.includes("--fail-fast");
 
+const ROOT = fromFileUrl(new URL("../", import.meta.url));
+
+// Matched against paths relative to ROOT, with `/` separators.
+const SKIP = [
+  /unstable/,
+  /^dotenv\/load\.ts$/,
+  /^front_matter\/yaml\.ts$/,
+  /^front_matter\/json\.ts$/,
+  /^front_matter\/toml\.ts$/,
+  /^front_matter\/any\.ts$/,
+  /^uuid\/v1\.ts$/,
+  /^uuid\/v3\.ts$/,
+  /^uuid\/v4\.ts$/,
+  /^uuid\/v5\.ts$/,
+  /^uuid\/v7\.ts$/,
+  /_test\.ts$/,
+  /_bench\.ts$/,
+  /\.d\.ts$/,
+  /\/_/,
+  /\/mod\.ts$/,
+];
+
 let shouldFail = false;
 
 const MOD_FILE_PATHS = (await getEntrypoints())
@@ -24,7 +47,7 @@ for (const modFilePath of MOD_FILE_PATHS) {
     modSource,
     ts.ScriptTarget.Latest,
   );
-  const modExportSpecifiers = new Set();
+  const modExportSpecifiers = new Set<string>();
   modSourceFile.forEachChild((node) => {
     if (
       ts.isExportDeclaration(node) &&
@@ -40,29 +63,12 @@ for (const modFilePath of MOD_FILE_PATHS) {
       exts: [".ts"],
       includeDirs: false,
       maxDepth: 1,
-      skip: [
-        /unstable/,
-        /dotenv(\/|\\)load\.ts$/,
-        /front_matter(\/|\\)yaml\.ts$/,
-        /front_matter(\/|\\)json\.ts$/,
-        /front_matter(\/|\\)toml\.ts$/,
-        /front_matter(\/|\\)any\.ts$/,
-        /uuid(\/|\\)v1\.ts$/,
-        /uuid(\/|\\)v3\.ts$/,
-        /uuid(\/|\\)v4\.ts$/,
-        /uuid(\/|\\)v5\.ts$/,
-        /uuid(\/|\\)v6\.ts$/,
-        /uuid(\/|\\)v7\.ts$/,
-        /_test\.ts$/,
-        /_bench\.ts$/,
-        /\.d\.ts$/,
-        /(\/|\\)_/,
-        /mod\.ts$/,
-      ],
     })
   ) {
-    const relativeSpecifier = relative(modFilePath, filePath).slice(1)
-      .replaceAll("\\", "/");
+    const relativePath = relative(ROOT, filePath).replaceAll("\\", "/");
+    if (SKIP.some((pattern) => pattern.test(relativePath))) continue;
+
+    const relativeSpecifier = `./${basename(filePath)}`;
 
     if (!modExportSpecifiers.has(relativeSpecifier)) {
       if (