diff --git a/cli/tsc/dts/lib.deno.ns.d.ts b/cli/tsc/dts/lib.deno.ns.d.ts
index 8759306dfe..cc069ed989 100644
--- a/cli/tsc/dts/lib.deno.ns.d.ts
+++ b/cli/tsc/dts/lib.deno.ns.d.ts
@@ -2100,6 +2100,9 @@ declare namespace Deno {
    * console.log(await Deno.seek(file.rid, -2, Deno.SeekMode.End)); // "9" (i.e. 11-2)
    * ```
    *
+   * @deprecated Use `file.seek()` instead. {@linkcode Deno.seek} will be
+   * removed in Deno 2.0.
+   *
    * @category I/O
    */
   export function seek(
@@ -2145,6 +2148,9 @@ declare namespace Deno {
    * console.log(Deno.seekSync(file.rid, -2, Deno.SeekMode.End)); // "9" (i.e. 11-2)
    * ```
    *
+   * @deprecated Use `file.seekSync()` instead. {@linkcode Deno.seekSync}
+   * will be removed in Deno 2.0.
+   *
    * @category I/O
    */
   export function seekSync(
diff --git a/runtime/js/90_deno_ns.js b/runtime/js/90_deno_ns.js
index 452c62725d..24e73d30e7 100644
--- a/runtime/js/90_deno_ns.js
+++ b/runtime/js/90_deno_ns.js
@@ -109,8 +109,22 @@ const denoNs = {
   stdin: io.stdin,
   stdout: io.stdout,
   stderr: io.stderr,
-  seek: fs.seek,
-  seekSync: fs.seekSync,
+  seek(rid, offset, whence) {
+    internals.warnOnDeprecatedApi(
+      "Deno.seek()",
+      new Error().stack,
+      "Use `file.seek()` instead.",
+    );
+    return fs.seek(rid, offset, whence);
+  },
+  seekSync(rid, offset, whence) {
+    internals.warnOnDeprecatedApi(
+      "Deno.seekSync()",
+      new Error().stack,
+      "Use `file.seekSync()` instead.",
+    );
+    return fs.seekSync(rid, offset, whence);
+  },
   connect: net.connect,
   listen: net.listen,
   loadavg: os.loadavg,