diff --git a/assert/equals.ts b/assert/equals.ts
index b8370584425b..7e800851d616 100644
--- a/assert/equals.ts
+++ b/assert/equals.ts
@@ -64,5 +64,20 @@ export function assertEquals<T>(
   const diffMsg = buildMessage(diffResult, { stringDiff }, arguments[3])
     .join("\n");
   message = `${message}\n${diffMsg}`;
+  // #6878: if the diff shows no removed/added lines, the values stringify
+  // identically but were still deemed unequal — typically because at least
+  // one nested property is a function (or Promise / Request / Blob / etc.)
+  // that gets compared by reference. The empty diff is confusing, so append
+  // a hint pointing at the likely cause.
+  if (
+    !stringDiff &&
+    diffResult.every((r) => r.type !== "added" && r.type !== "removed")
+  ) {
+    message = `${message}\n` +
+      "    Note: values stringify identically but are not structurally equal. " +
+      "Functions, Promises, Requests, Blobs, and other built-ins are compared by " +
+      "reference, so two distinct instances are never equal even when their " +
+      "representations match.";
+  }
   throw new AssertionError(message);
 }
diff --git a/assert/equals_test.ts b/assert/equals_test.ts
index 8f23661d6b2f..6cfb7de95f5a 100644
--- a/assert/equals_test.ts
+++ b/assert/equals_test.ts
@@ -1,5 +1,10 @@
 // Copyright 2018-2026 the Deno authors. MIT license.
-import { assertEquals, AssertionError, assertThrows } from "./mod.ts";
+import {
+  assertEquals,
+  AssertionError,
+  assertStringIncludes,
+  assertThrows,
+} from "./mod.ts";
 import {
   bold,
   gray,
@@ -207,6 +212,48 @@ Deno.test({
   },
 });
 
+Deno.test({
+  name:
+    "assertEquals() hints at reference-equality when objects with function props stringify identically (#6878)",
+  fn() {
+    let caught: AssertionError | undefined;
+    try {
+      assertEquals(
+        { x: 1, y: () => 2 },
+        { x: 1, y: () => 2 },
+      );
+    } catch (e) {
+      caught = e as AssertionError;
+    }
+    if (!caught) throw new Error("Expected assertEquals to throw");
+    assertStringIncludes(caught.message, "Values are not equal");
+    assertStringIncludes(
+      caught.message,
+      "stringify identically but are not structurally equal",
+    );
+    assertStringIncludes(caught.message, "compared by reference");
+  },
+});
+
+Deno.test({
+  name:
+    "assertEquals() does not append reference-equality hint when there is a real textual diff",
+  fn() {
+    let caught: AssertionError | undefined;
+    try {
+      assertEquals({ x: 1 }, { x: 2 });
+    } catch (e) {
+      caught = e as AssertionError;
+    }
+    if (!caught) throw new Error("Expected assertEquals to throw");
+    assertEquals(
+      caught.message.includes("stringify identically"),
+      false,
+      "Hint should only fire when the diff is empty",
+    );
+  },
+});
+
 Deno.test({
   name: "assertEquals() matches same Set with object keys",
   fn() {