diff --git a/.changeset/smart-fans-crash.md b/.changeset/smart-fans-crash.md
new file mode 100644
index 0000000000..ca38575acb
--- /dev/null
+++ b/.changeset/smart-fans-crash.md
@@ -0,0 +1,5 @@
+---
+'svelte': patch
+---
+
+fix: correctly compile $effect.root in svelte modules
diff --git a/packages/svelte/src/compiler/phases/3-transform/server/transform-server.js b/packages/svelte/src/compiler/phases/3-transform/server/transform-server.js
index b9d6a5bc4d..581d4dcd03 100644
--- a/packages/svelte/src/compiler/phases/3-transform/server/transform-server.js
+++ b/packages/svelte/src/compiler/phases/3-transform/server/transform-server.js
@@ -411,6 +411,14 @@ const global_visitors = {
 			return b.literal(false);
 		}
 
+		if (rune === '$effect.root') {
+			const args = /** @type {import('estree').Expression[]} */ (
+				node.arguments.map((arg) => context.visit(arg))
+			);
+			// Just call the function directly
+			return b.call(args[0]);
+		}
+
 		if (rune === '$state.snapshot') {
 			return /** @type {import('estree').Expression} */ (context.visit(node.arguments[0]));
 		}
@@ -571,7 +579,7 @@ const javascript_visitors_runes = {
 		for (const declarator of node.declarations) {
 			const init = declarator.init;
 			const rune = get_rune(init, state.scope);
-			if (!rune || rune === '$effect.tracking' || rune === '$inspect') {
+			if (!rune || rune === '$effect.tracking' || rune === '$inspect' || rune === '$effect.root') {
 				declarations.push(/** @type {import('estree').VariableDeclarator} */ (visit(declarator)));
 				continue;
 			}
diff --git a/packages/svelte/tests/runtime-runes/samples/effect-root-3/_config.js b/packages/svelte/tests/runtime-runes/samples/effect-root-3/_config.js
new file mode 100644
index 0000000000..fa69197903
--- /dev/null
+++ b/packages/svelte/tests/runtime-runes/samples/effect-root-3/_config.js
@@ -0,0 +1,30 @@
+import { flushSync } from 'svelte';
+import { test } from '../../test';
+
+export default test({
+	html: '<button>0</button><button>0</button><button>cleanup</button>',
+
+	async test({ assert, target, logs }) {
+		const [b1, b2, b3] = target.querySelectorAll('button');
+
+		flushSync(() => {
+			b1.click();
+			b2.click();
+		});
+
+		assert.deepEqual(logs, [0, 1]);
+
+		flushSync(() => {
+			b3.click();
+		});
+
+		assert.deepEqual(logs, [0, 1, 'cleanup 1', 'cleanup 2']);
+
+		flushSync(() => {
+			b1.click();
+			b2.click();
+		});
+
+		assert.deepEqual(logs, [0, 1, 'cleanup 1', 'cleanup 2']);
+	}
+});
diff --git a/packages/svelte/tests/runtime-runes/samples/effect-root-3/main.svelte b/packages/svelte/tests/runtime-runes/samples/effect-root-3/main.svelte
new file mode 100644
index 0000000000..fb37dfe47d
--- /dev/null
+++ b/packages/svelte/tests/runtime-runes/samples/effect-root-3/main.svelte
@@ -0,0 +1,11 @@
+<script>
+	import { with_root } from './root.svelte.js';
+	let x = $state(0);
+	let y = $state(0);
+
+	const cleanup = with_root(() => x)
+</script>
+
+<button onclick={() => x++}>{x}</button>
+<button onclick={() => y++}>{y}</button>
+<button onclick={cleanup}>cleanup</button>
diff --git a/packages/svelte/tests/runtime-runes/samples/effect-root-3/root.svelte.js b/packages/svelte/tests/runtime-runes/samples/effect-root-3/root.svelte.js
new file mode 100644
index 0000000000..4e05cdf8ef
--- /dev/null
+++ b/packages/svelte/tests/runtime-runes/samples/effect-root-3/root.svelte.js
@@ -0,0 +1,20 @@
+export function with_root(get_x) {
+	const cleanup = $effect.root(() => {
+		$effect(() => {
+			console.log(get_x());
+		});
+
+		const nested_cleanup = $effect.root(() => {
+			return () => {
+				console.log('cleanup 2');
+			};
+		});
+
+		return () => {
+			console.log('cleanup 1');
+			nested_cleanup();
+		};
+	});
+
+	return cleanup;
+}