diff --git a/.changeset/fair-crabs-check.md b/.changeset/fair-crabs-check.md
new file mode 100644
index 0000000000..fa51ebf2d5
--- /dev/null
+++ b/.changeset/fair-crabs-check.md
@@ -0,0 +1,5 @@
+---
+'svelte': patch
+---
+
+fix: prevent false positives when detecting runes mode
diff --git a/packages/svelte/src/compiler/phases/2-analyze/index.js b/packages/svelte/src/compiler/phases/2-analyze/index.js
index c0c8906acc..2920a92610 100644
--- a/packages/svelte/src/compiler/phases/2-analyze/index.js
+++ b/packages/svelte/src/compiler/phases/2-analyze/index.js
@@ -284,7 +284,11 @@ export function analyze_component(root, options) {
 				if (declaration === null && /[a-z]/.test(store_name[0])) {
 					error(references[0].node, 'illegal-global', name);
 				} else if (declaration !== null && Runes.includes(name)) {
-					warn(warnings, declaration.node, [], 'store-with-rune-name', store_name);
+					for (const { node, path } of references) {
+						if (path.at(-1)?.type === 'CallExpression') {
+							warn(warnings, node, [], 'store-with-rune-name', store_name);
+						}
+					}
 				}
 			}
 
@@ -302,6 +306,8 @@ export function analyze_component(root, options) {
 
 			const binding = instance.scope.declare(b.id(name), 'store_sub', 'synthetic');
 			binding.references = references;
+			instance.scope.references.set(name, references);
+			module.scope.references.delete(name);
 		}
 	}
 
diff --git a/packages/svelte/tests/validator/samples/store-looking-like-rune/input.svelte b/packages/svelte/tests/validator/samples/store-looking-like-rune/input.svelte
new file mode 100644
index 0000000000..d5d0f76942
--- /dev/null
+++ b/packages/svelte/tests/validator/samples/store-looking-like-rune/input.svelte
@@ -0,0 +1,8 @@
+<script>
+	import { writable } from 'svelte/store';
+
+	export let initial;
+	const state = writable(initial);
+</script>
+
+<div>{$state}</div>
diff --git a/packages/svelte/tests/validator/samples/store-looking-like-rune/warnings.json b/packages/svelte/tests/validator/samples/store-looking-like-rune/warnings.json
new file mode 100644
index 0000000000..fe51488c70
--- /dev/null
+++ b/packages/svelte/tests/validator/samples/store-looking-like-rune/warnings.json
@@ -0,0 +1 @@
+[]
diff --git a/packages/svelte/tests/validator/samples/store-runes-conflict/warnings.json b/packages/svelte/tests/validator/samples/store-runes-conflict/warnings.json
index 534a5e1983..58236d814b 100644
--- a/packages/svelte/tests/validator/samples/store-runes-conflict/warnings.json
+++ b/packages/svelte/tests/validator/samples/store-runes-conflict/warnings.json
@@ -3,12 +3,12 @@
 		"code": "store-with-rune-name",
 		"message": "It looks like you're using the $state rune, but there is a local binding called state. Referencing a local variable with a $ prefix will create a store subscription. Please rename state to avoid the ambiguity.",
 		"start": {
-			"column": 7,
-			"line": 2
+			"column": 1,
+			"line": 3
 		},
 		"end": {
-			"column": 12,
-			"line": 2
+			"column": 7,
+			"line": 3
 		}
 	}
 ]