diff --git a/.changeset/slimy-frogs-share.md b/.changeset/slimy-frogs-share.md
new file mode 100644
index 0000000000..27a393d564
--- /dev/null
+++ b/.changeset/slimy-frogs-share.md
@@ -0,0 +1,5 @@
+---
+'svelte': patch
+---
+
+fix: avoid false-positive batch invariant error
diff --git a/packages/svelte/src/internal/client/reactivity/batch.js b/packages/svelte/src/internal/client/reactivity/batch.js
index a5c9a51eec..ae4f5a6dac 100644
--- a/packages/svelte/src/internal/client/reactivity/batch.js
+++ b/packages/svelte/src/internal/client/reactivity/batch.js
@@ -679,7 +679,9 @@ export class Batch {
 					batch.discard();
 				}
 			} else if (sources.length > 0) {
-				if (DEV) {
+				// The microtask queue can contain the batch already scheduled to run right
+				// after this one is finished, so throwing the invariant would be wrong here.
+				if (DEV && !batch.#decrement_queued) {
 					invariant(batch.#roots.length === 0, 'Batch has scheduled roots');
 				}
 
@@ -732,7 +734,8 @@ export class Batch {
 				}
 
 				// Only apply and traverse when we know we triggered async work with marking the effects
-				if (batch.#roots.length > 0) {
+				// and know this won't run anyway right afterwards
+				if (batch.#roots.length > 0 && !batch.#decrement_queued) {
 					batch.apply();
 
 					for (var root of batch.#roots) {
diff --git a/packages/svelte/tests/runtime-runes/samples/async-pending-batch/_config.js b/packages/svelte/tests/runtime-runes/samples/async-pending-batch/_config.js
new file mode 100644
index 0000000000..e7359efa2d
--- /dev/null
+++ b/packages/svelte/tests/runtime-runes/samples/async-pending-batch/_config.js
@@ -0,0 +1,16 @@
+import { tick } from 'svelte';
+import { test } from '../../test';
+
+export default test({
+	// This test mainly checks that we don't run into the 'Batch has scheduled roots' invariant wrongly.
+	// It is crafted such that two batches are scheduled to run in the same microtask, and the first
+	// tries to rebase the second.
+	async test({ assert, target }) {
+		await tick();
+		const [run] = target.querySelectorAll('button');
+
+		run.click();
+		await tick();
+		assert.htmlEqual(target.innerHTML, '<button>run</button> none none 0');
+	}
+});
diff --git a/packages/svelte/tests/runtime-runes/samples/async-pending-batch/main.svelte b/packages/svelte/tests/runtime-runes/samples/async-pending-batch/main.svelte
new file mode 100644
index 0000000000..19305cfb76
--- /dev/null
+++ b/packages/svelte/tests/runtime-runes/samples/async-pending-batch/main.svelte
@@ -0,0 +1,8 @@
+<script>
+	let selectedId = $state(1);
+	let selectedOption = $derived(selectedId ? await selectedId : null);
+</script>
+
+<button onclick={() => (selectedId = null)}>run</button>
+
+{selectedId ?? "none"} {selectedOption ?? "none"} {$effect.pending()}