diff --git a/.changeset/tangy-women-shout.md b/.changeset/tangy-women-shout.md
new file mode 100644
index 0000000000..f62d799d93
--- /dev/null
+++ b/.changeset/tangy-women-shout.md
@@ -0,0 +1,5 @@
+---
+'svelte': patch
+---
+
+fix: remove nodes in boundary when work is pending and HMR is active
diff --git a/packages/svelte/src/internal/client/dev/hmr.js b/packages/svelte/src/internal/client/dev/hmr.js
index 9fa4e6ccbd..071901aafc 100644
--- a/packages/svelte/src/internal/client/dev/hmr.js
+++ b/packages/svelte/src/internal/client/dev/hmr.js
@@ -6,6 +6,8 @@ import { block, branch, destroy_effect } from '../reactivity/effects.js';
 import { set, source } from '../reactivity/sources.js';
 import { set_should_intro } from '../render.js';
 import { get } from '../runtime.js';
+import { assign_nodes } from '../dom/template.js';
+import { create_comment } from '../dom/operations.js';
 
 /**
  * @template {(anchor: Comment, props: any) => any} Component
@@ -27,6 +29,13 @@ export function hmr(fn) {
 
 		let ran = false;
 
+		// Surround the wrapped effects with comments and assign the nodes
+		// on the wrapping effects so the parent can properly do DOM operations.
+		let start = create_comment();
+		let end = create_comment();
+
+		anchor.before(start);
+
 		block(() => {
 			if (component === (component = get(current))) {
 				return;
@@ -61,6 +70,10 @@ export function hmr(fn) {
 			anchor = hydrate_node;
 		}
 
+		anchor.before(end);
+
+		assign_nodes(start, end);
+
 		return instance;
 	}