diff --git a/.changeset/selfish-trainers-kiss.md b/.changeset/selfish-trainers-kiss.md
new file mode 100644
index 0000000000..40e781e20f
--- /dev/null
+++ b/.changeset/selfish-trainers-kiss.md
@@ -0,0 +1,5 @@
+---
+'svelte': patch
+---
+
+fix: ensure inner script tags are properly removed
diff --git a/packages/svelte/src/internal/client/dom/template.js b/packages/svelte/src/internal/client/dom/template.js
index 767bb5bdd0..0b927071d0 100644
--- a/packages/svelte/src/internal/client/dom/template.js
+++ b/packages/svelte/src/internal/client/dom/template.js
@@ -187,26 +187,41 @@ function run_scripts(node) {
 	// scripts were SSR'd, in which case they will run
 	if (hydrating) return;
 
+	const is_fragment = node.nodeType === 11;
 	const scripts =
 		/** @type {HTMLElement} */ (node).tagName === 'SCRIPT'
 			? [/** @type {HTMLScriptElement} */ (node)]
 			: node.querySelectorAll('script');
+	const effect = /** @type {Effect} */ (current_effect);
+
 	for (const script of scripts) {
-		var clone = document.createElement('script');
+		const clone = document.createElement('script');
 		for (var attribute of script.attributes) {
 			clone.setAttribute(attribute.name, attribute.value);
 		}
 
 		clone.textContent = script.textContent;
 
+		const replace = () => {
+			// The script has changed - if it's at the edges, the effect now points at dead nodes
+			if (is_fragment ? node.firstChild === script : node === script) {
+				effect.nodes_start = clone;
+			}
+			if (is_fragment ? node.lastChild === script : node === script) {
+				effect.nodes_end = clone;
+			}
+
+			script.replaceWith(clone);
+		};
+
 		// If node === script tag, replaceWith will do nothing because there's no parent yet,
 		// waiting until that's the case using an effect solves this.
 		// Don't do it in other circumstances or we could accidentally execute scripts
 		// in an adjacent @html tag that was instantiated in the meantime.
 		if (script === node) {
-			queue_micro_task(() => script.replaceWith(clone));
+			queue_micro_task(replace);
 		} else {
-			script.replaceWith(clone);
+			replace();
 		}
 	}
 }
diff --git a/packages/svelte/tests/runtime-browser/samples/sole-script-tag/_config.js b/packages/svelte/tests/runtime-browser/samples/sole-script-tag/_config.js
index 650e9241ea..ee1e810d30 100644
--- a/packages/svelte/tests/runtime-browser/samples/sole-script-tag/_config.js
+++ b/packages/svelte/tests/runtime-browser/samples/sole-script-tag/_config.js
@@ -4,8 +4,12 @@ export default test({
 	// Test that template with sole script tag does execute when instantiated in the client.
 	// Needs to be in this test suite because JSDOM does not quite get this right.
 	mode: ['client'],
-	test({ window, assert }) {
+	async test({ target, assert }) {
 		// In here to give effects etc time to execute
-		assert.htmlEqual(window.document.body.innerHTML, 'this should be executed');
+		assert.htmlEqual(target.querySelector('div')?.innerHTML || '', 'this should be executed');
+		// Check that the script tag is properly removed
+		target.querySelector('button')?.click();
+		await new Promise((r) => setTimeout(r, 100));
+		assert.equal(target.querySelector('script'), null);
 	}
 });
diff --git a/packages/svelte/tests/runtime-browser/samples/sole-script-tag/main.svelte b/packages/svelte/tests/runtime-browser/samples/sole-script-tag/main.svelte
index 509b36028d..eda4cee629 100644
--- a/packages/svelte/tests/runtime-browser/samples/sole-script-tag/main.svelte
+++ b/packages/svelte/tests/runtime-browser/samples/sole-script-tag/main.svelte
@@ -1,4 +1,11 @@
-<div></div>
-{#if true}
-    <script>document.body.innerHTML = 'this should be executed'</script>
+<script lang="ts">
+	let visible = $state(true);
+</script>
+
+<button onclick={() => (visible = false)}>hide</button>
+{#if visible}
+	<script>
+		document.body.querySelector('.after').innerHTML = 'this should be executed';
+	</script>
 {/if}
+<div class="after">after</div>