diff --git a/news/changelog-1.6.md b/news/changelog-1.6.md
index 042a99dea9f..1f460718eab 100644
--- a/news/changelog-1.6.md
+++ b/news/changelog-1.6.md
@@ -38,6 +38,7 @@ All changes included in 1.6:
 - ([#10761](https://github.com/quarto-dev/quarto-cli/issues/10761)): Add support for `licence: CC0` to automatically link to Creative Commons licence [CC0 1.0](https://creativecommons.org/publicdomain/zero/1.0/).
 - ([#10817](https://github.com/quarto-dev/quarto-cli/issues/10817)): Ensure that user provided SCSS has precedent over quarto generated scss also for dark theme.
 - ([#11124](https://github.com/quarto-dev/quarto-cli/pull/11124)): Use stable order of GLightbox options
+- ([#11401](https://github.com/quarto-dev/quarto-cli/issues/11401)): Use EJS comment syntax to hide internal TODO notes from the output.
 
 ## `revealjs` Format
 
diff --git a/src/resources/formats/html/templates/quarto-html.ejs b/src/resources/formats/html/templates/quarto-html.ejs
index 1e0c7487ebe..61d39d437aa 100644
--- a/src/resources/formats/html/templates/quarto-html.ejs
+++ b/src/resources/formats/html/templates/quarto-html.ejs
@@ -283,8 +283,10 @@ window.document.addEventListener("DOMContentLoaded", function (event) {
 
   
   if (window.document.getElementById('quarto-embedded-source-code-modal')) {
+    <% /* %>
     // For code content inside modals, clipBoardJS needs to be initialized with a container option
     // TODO: Check when it could be a function (https://github.com/zenorocha/clipboard.js/issues/860)
+    <% */ %>
     const clipboardModal = new window.ClipboardJS('.code-copy-button[data-in-quarto-modal]', {
       text: getTextToCopy,
       container: window.document.getElementById('quarto-embedded-source-code-modal')
@@ -507,7 +509,9 @@ window.document.addEventListener("DOMContentLoaded", function (event) {
       if (window.Quarto?.typesetMath) {
         window.Quarto.typesetMath(note);
       }
+      <% /* %>
       // TODO in 1.5, we should make sure this works without a callout special case
+      <% */ %>
       if (note.classList.contains("callout")) {
         return note.outerHTML;
       } else {
diff --git a/tests/docs/smoke-all/2024/11/14/issue-11401.qmd b/tests/docs/smoke-all/2024/11/14/issue-11401.qmd
new file mode 100644
index 00000000000..7e34be7495e
--- /dev/null
+++ b/tests/docs/smoke-all/2024/11/14/issue-11401.qmd
@@ -0,0 +1,11 @@
+---
+format: html
+_quarto:
+  tests:
+    html:
+      ensureFileRegexMatches:
+        - []
+        - ["TODO"]
+---
+
+## Hello, world
\ No newline at end of file