diff --git a/.changeset/nice-squids-sniff.md b/.changeset/nice-squids-sniff.md
new file mode 100644
index 0000000000..dd0dcf4d9e
--- /dev/null
+++ b/.changeset/nice-squids-sniff.md
@@ -0,0 +1,6 @@
+---
+"@pnpm/plugin-commands-rebuild": patch
+pnpm: patch
+---
+
+The `pnpm rebuild` command should not add pkgs included in `ignoredBuiltDependencies` to `ignoredBuilds` in `node_modules/.modules.yaml` [#9338](https://github.com/pnpm/pnpm/issues/9338).
diff --git a/exec/plugin-commands-rebuild/src/implementation/extendRebuildOptions.ts b/exec/plugin-commands-rebuild/src/implementation/extendRebuildOptions.ts
index ad0eeefa60..9f58df84f5 100644
--- a/exec/plugin-commands-rebuild/src/implementation/extendRebuildOptions.ts
+++ b/exec/plugin-commands-rebuild/src/implementation/extendRebuildOptions.ts
@@ -51,7 +51,7 @@ export type StrictRebuildOptions = {
   peersSuffixMaxLength: number
   strictStorePkgContentCheck: boolean
   fetchFullMetadata?: boolean
-} & Pick<Config, 'sslConfigs' | 'onlyBuiltDependencies' | 'onlyBuiltDependenciesFile' | 'neverBuiltDependencies'>
+} & Pick<Config, 'sslConfigs' | 'onlyBuiltDependencies' | 'onlyBuiltDependenciesFile' | 'neverBuiltDependencies' | 'ignoredBuiltDependencies'>
 
 export type RebuildOptions = Partial<StrictRebuildOptions> &
 Pick<StrictRebuildOptions, 'storeDir' | 'storeController'> & Pick<Config, 'rootProjectManifest' | 'rootProjectManifestDir'>
diff --git a/exec/plugin-commands-rebuild/src/implementation/index.ts b/exec/plugin-commands-rebuild/src/implementation/index.ts
index bf9f70afbf..5c96c73307 100644
--- a/exec/plugin-commands-rebuild/src/implementation/index.ts
+++ b/exec/plugin-commands-rebuild/src/implementation/index.ts
@@ -310,7 +310,9 @@ async function _rebuild (
   const _allowBuild = createAllowBuildFunction(opts) ?? (() => true)
   const allowBuild = (pkgName: string) => {
     if (_allowBuild(pkgName)) return true
-    ignoredPkgs.push(pkgName)
+    if (!opts.ignoredBuiltDependencies?.includes(pkgName)) {
+      ignoredPkgs.push(pkgName)
+    }
     return false
   }
   const builtDepPaths = new Set<string>()