diff --git a/changelog_unreleased/markdown/19739.md b/changelog_unreleased/markdown/19739.md
new file mode 100644
index 000000000..a4ed6a496
--- /dev/null
+++ b/changelog_unreleased/markdown/19739.md
@@ -0,0 +1,15 @@
+#### Preserve single tildes in Markdown (#19739 by @lazerg)
+
+Since 3.9.0, single-tilde spans like `H~2~O` were rewritten to double tildes, turning subscript syntax into strike-through. Only double tildes are treated that way now, matching GitHub.
+
+<!-- prettier-ignore -->
+```markdown
+<!-- Input -->
+H~2~O
+
+<!-- Prettier stable -->
+H~~2~~O
+
+<!-- Prettier main -->
+H~2~O
+```
diff --git a/src/language-markdown/parse/parse-markdown.js b/src/language-markdown/parse/parse-markdown.js
index 8c07cc832..ba7f76a2b 100644
--- a/src/language-markdown/parse/parse-markdown.js
+++ b/src/language-markdown/parse/parse-markdown.js
@@ -16,7 +16,7 @@ let markdownParseOptions;
 function getMarkdownParseOptions() {
   return (markdownParseOptions ??= {
     extensions: [
-      gfmSyntax(),
+      gfmSyntax({ singleTilde: false }),
       mathSyntax(),
       wikiLinkSyntax({
         // We don't need support alias, use a fake string to bypass
diff --git a/tests/format/markdown/delete/__snapshots__/format.test.js.snap b/tests/format/markdown/delete/__snapshots__/format.test.js.snap
index 7d3bc7d0c..07a25aa94 100644
--- a/tests/format/markdown/delete/__snapshots__/format.test.js.snap
+++ b/tests/format/markdown/delete/__snapshots__/format.test.js.snap
@@ -13,3 +13,21 @@ proseWrap: "always"
 
 ================================================================================
 `;
+
+exports[`single-tilde.md - {"proseWrap":"always"} format 1`] = `
+====================================options=====================================
+parsers: ["markdown"]
+proseWrap: "always"
+                                                      printWidth: 80 (default) |
+=====================================input======================================
+H~2~O
+
+~~2~~ and ~1~ and ~~~3~~~ and ~~~~4~~~~
+
+=====================================output=====================================
+H~2~O
+
+~~2~~ and ~1~ and ~~~3~~~ and ~~~~4~~~~
+
+================================================================================
+`;
diff --git a/tests/format/markdown/delete/single-tilde.md b/tests/format/markdown/delete/single-tilde.md
new file mode 100644
index 000000000..262b98b8d
--- /dev/null
+++ b/tests/format/markdown/delete/single-tilde.md
@@ -0,0 +1,3 @@
+H~2~O
+
+~~2~~ and ~1~ and ~~~3~~~ and ~~~~4~~~~
diff --git a/tests/format/markdown/gfm-test-suite/__snapshots__/format.test.js.snap b/tests/format/markdown/gfm-test-suite/__snapshots__/format.test.js.snap
index f306edc49..e6a5b81cf 100644
--- a/tests/format/markdown/gfm-test-suite/__snapshots__/format.test.js.snap
+++ b/tests/format/markdown/gfm-test-suite/__snapshots__/format.test.js.snap
@@ -300,7 +300,7 @@ proseWrap: "always"
 ~~Hi~~ Hello, ~there~ world!
 
 =====================================output=====================================
-~~Hi~~ Hello, ~~there~~ world!
+~~Hi~~ Hello, ~there~ world!
 
 ================================================================================
 `;