diff --git a/news/changelog-1.9.md b/news/changelog-1.9.md
index 9c327bc5e1d..a78022004f2 100644
--- a/news/changelog-1.9.md
+++ b/news/changelog-1.9.md
@@ -128,3 +128,4 @@ All changes included in 1.9:
 - ([#13575](https://github.com/quarto-dev/quarto-cli/pull/13575)): Improve CPU architecture detection/reporting in macOS to allow quarto to run in virtualized environments such as OpenAI's `codex`.
 - ([#13656](https://github.com/quarto-dev/quarto-cli/issues/13656)): Fix R code cells with empty `lang: ""` option producing invalid markdown class attributes.
 - ([#13832](https://github.com/quarto-dev/quarto-cli/pull/13832)): Fix `license.text` metadata not being accessible when using an inline license (`license: "text"`), and populate it with the license name for CC licenses instead of empty string. (author: @mcanouil)
+- ([#13890](https://github.com/quarto-dev/quarto-cli/issues/13890)): Fix render failure when using `embed-resources: true` with input path through a symlinked directory. The cleanup now resolves symlinks before comparing paths.
diff --git a/src/deno_ral/fs.ts b/src/deno_ral/fs.ts
index e48e1c68ca9..05bc526b4f1 100644
--- a/src/deno_ral/fs.ts
+++ b/src/deno_ral/fs.ts
@@ -8,6 +8,7 @@ import { fromFileUrl } from "./path.ts";
 import { resolve, SEP as SEPARATOR } from "./path.ts";
 import { copySync } from "fs/copy";
 import { existsSync } from "fs/exists";
+import { originalRealPathSync } from "./original-real-path.ts";
 
 export { ensureDir, ensureDirSync } from "fs/ensure-dir";
 export { existsSync } from "fs/exists";
@@ -132,7 +133,26 @@ export function safeRemoveDirSync(
   path: string,
   boundary: string,
 ) {
-  if (path === boundary || !isSubdir(boundary, path)) {
+  // Resolve symlinks to ensure consistent path comparison.
+  // This is needed because external tools (like knitr) may resolve symlinks
+  // while project.dir preserves them.
+  //
+  // We use the original Deno.realPathSync (saved before monkey-patching)
+  // because the monkey-patch replaces it with normalizePath which doesn't
+  // resolve symlinks.
+  //
+  // Note: The UNC path bug that motivated the monkey-patch was fixed in
+  // Deno v1.16 (see denoland/deno#12243), so this is safe on all platforms.
+  let resolvedPath = path;
+  let resolvedBoundary = boundary;
+  try {
+    resolvedPath = originalRealPathSync(path);
+    resolvedBoundary = originalRealPathSync(boundary);
+  } catch {
+    // If resolution fails (e.g., path doesn't exist), use original paths
+  }
+
+  if (resolvedPath === resolvedBoundary || !isSubdir(resolvedBoundary, resolvedPath)) {
     throw new UnsafeRemovalError(
       `Refusing to remove directory ${path} that isn't a subdirectory of ${boundary}`,
     );
diff --git a/src/deno_ral/original-real-path.ts b/src/deno_ral/original-real-path.ts
new file mode 100644
index 00000000000..e2c315ca642
--- /dev/null
+++ b/src/deno_ral/original-real-path.ts
@@ -0,0 +1,12 @@
+/*
+ * original-real-path.ts
+ *
+ * Copyright (C) 2020-2025 Posit Software, PBC
+ *
+ * Saves original Deno.realPathSync before monkey-patching.
+ * This module MUST be imported in quarto.ts BEFORE monkey-patch.ts.
+ *
+ * DO NOT add any imports to this file - it must remain dependency-free
+ * to avoid circular import issues.
+ */
+export const originalRealPathSync: typeof Deno.realPathSync = Deno.realPathSync;
diff --git a/src/quarto.ts b/src/quarto.ts
index f421bf2ed6f..616bf8928be 100644
--- a/src/quarto.ts
+++ b/src/quarto.ts
@@ -4,6 +4,8 @@
  * Copyright (C) 2020-2022 Posit Software, PBC
  */
 
+// Must be FIRST to save original Deno.realPathSync before monkey-patching
+import "./deno_ral/original-real-path.ts";
 import "./core/deno/monkey-patch.ts";
 
 import {
diff --git a/tests/docs/render/symlink-embed-resources/test.qmd b/tests/docs/render/symlink-embed-resources/test.qmd
new file mode 100644
index 00000000000..8948f0ddec0
--- /dev/null
+++ b/tests/docs/render/symlink-embed-resources/test.qmd
@@ -0,0 +1,13 @@
+---
+format:
+  html:
+    embed-resources: true
+---
+
+# Test Document
+
+This tests rendering via symlinked directory with embed-resources.
+
+```{r}
+plot(1:10)
+```
diff --git a/tests/smoke/render/render-symlink-embed-resources.test.ts b/tests/smoke/render/render-symlink-embed-resources.test.ts
new file mode 100644
index 00000000000..f9395cb4f4a
--- /dev/null
+++ b/tests/smoke/render/render-symlink-embed-resources.test.ts
@@ -0,0 +1,54 @@
+/*
+ * render-symlink-embed-resources.test.ts
+ *
+ * Regression test for https://github.com/quarto-dev/quarto-cli/issues/13890
+ *
+ * When rendering a qmd via a symlinked path with embed-resources: true,
+ * the cleanup should not fail due to path mismatch between symlink and real path.
+ *
+ * Copyright (C) 2020-2025 Posit Software, PBC
+ */
+
+import { testQuartoCmd } from "../../test.ts";
+import { noErrors, fileExists } from "../../verify.ts";
+import { docs } from "../../utils.ts";
+import { join, dirname, resolve } from "../../../src/deno_ral/path.ts";
+import { existsSync } from "../../../src/deno_ral/fs.ts";
+import { isWindows } from "../../../src/deno_ral/platform.ts";
+
+const testDir = docs("render/symlink-embed-resources");
+const testFile = "test.qmd";
+const symlinkDir = join(dirname(testDir), "symlink-embed-resources-link");
+
+testQuartoCmd(
+  "render",
+  [join(symlinkDir, testFile)],
+  [
+    noErrors,
+    fileExists(join(symlinkDir, "test.html")),
+  ],
+  {
+    ignore: isWindows,
+    setup: async () => {
+      if (existsSync(symlinkDir)) {
+        await Deno.remove(symlinkDir);
+      }
+      // Use absolute paths for symlink to ensure correct resolution
+      Deno.symlinkSync(resolve(testDir), resolve(symlinkDir));
+    },
+    teardown: async () => {
+      const htmlViaSymlink = join(symlinkDir, "test.html");
+      if (existsSync(htmlViaSymlink)) {
+        await Deno.remove(htmlViaSymlink);
+      }
+      if (existsSync(symlinkDir)) {
+        await Deno.remove(symlinkDir);
+      }
+      const realHtml = join(testDir, "test.html");
+      if (existsSync(realHtml)) {
+        await Deno.remove(realHtml);
+      }
+    },
+  },
+  "Render via symlink with embed-resources (issue #13890)",
+);
diff --git a/tests/unit/ral/safe-remove-dir.test.ts b/tests/unit/ral/safe-remove-dir.test.ts
index 984a7945825..e08300299fe 100644
--- a/tests/unit/ral/safe-remove-dir.test.ts
+++ b/tests/unit/ral/safe-remove-dir.test.ts
@@ -11,6 +11,7 @@ import { assert, assertThrows } from "testing/asserts";
 import { createTempContext } from "../../../src/core/temp.ts";
 import { ensureDirSync, safeRemoveDirSync } from "../../../src/deno_ral/fs.ts";
 import { join } from "../../../src/deno_ral/path.ts";
+import { isWindows } from "../../../src/deno_ral/platform.ts";
 
 unitTest("safeRemoveDirSync", async () => {
 
@@ -30,3 +31,31 @@ unitTest("safeRemoveDirSync", async () => {
 
   temp.cleanup();
 });
+
+unitTest("safeRemoveDirSync with symlinks", async () => {
+  const temp = createTempContext();
+
+  const realDir = temp.createDir();
+  const projectRoot = join(realDir, "project-root");
+  const subDir = join(projectRoot, "test_files");
+  ensureDirSync(projectRoot);
+  ensureDirSync(subDir);
+
+  const symlinkPath = join(realDir, "project-symlink");
+  Deno.symlinkSync(projectRoot, symlinkPath);
+
+  // Test: path via symlink, boundary via real path - should succeed
+  const pathViaSymlink = join(symlinkPath, "test_files");
+  safeRemoveDirSync(pathViaSymlink, projectRoot);
+
+  // Recreate for next test
+  ensureDirSync(subDir);
+
+  // Test: path via real path, boundary via symlink - should succeed
+  safeRemoveDirSync(subDir, symlinkPath);
+
+  // Cleanup symlink
+  Deno.removeSync(symlinkPath);
+
+  temp.cleanup();
+}, { ignore: isWindows });