diff --git a/packages/desktop/package.json b/packages/desktop/package.json
index f79bc5db4..dfb0b587c 100644
--- a/packages/desktop/package.json
+++ b/packages/desktop/package.json
@@ -58,7 +58,7 @@
   "//": "The packages not bundled with bin/dump_artifacts.js must be specified here as the runtime dependencies. See `scripts/build_bin.js` for the details.",
   "dependencies": {
     "fs-extra": "^11.2.0",
-    "pyodide": "0.28.2",
+    "pyodide": "0.29.0",
     "yargs": "^18.0.0"
   },
   "devDependencies": {
diff --git a/packages/kernel/package.json b/packages/kernel/package.json
index a2302ad5e..1897c4952 100644
--- a/packages/kernel/package.json
+++ b/packages/kernel/package.json
@@ -71,7 +71,7 @@
     "eslint-plugin-react": "^7.37.5",
     "eslint-plugin-react-hooks": "^7.0.1",
     "prettier": "^3.6.2",
-    "pyodide": "0.28.2",
+    "pyodide": "0.29.0",
     "typescript": "^5.9.2",
     "typescript-eslint": "^8.46.2",
     "vitest": "^4.0.15"
diff --git a/yarn.lock b/yarn.lock
index 29a0b45c0..38c1f985f 100644
--- a/yarn.lock
+++ b/yarn.lock
@@ -5474,7 +5474,7 @@ __metadata:
     glob: "npm:^13.0.0"
     node-html-parser: "npm:^7.0.1"
     prettier: "npm:^3.6.2"
-    pyodide: "npm:0.28.2"
+    pyodide: "npm:0.29.0"
     react: "npm:^18.2.0"
     react-dom: "npm:^18.2.0"
     rimraf: "npm:^6.0.1"
@@ -5525,7 +5525,7 @@ __metadata:
     eslint-plugin-react-hooks: "npm:^7.0.1"
     path-browserify: "npm:^1.0.1"
     prettier: "npm:^3.6.2"
-    pyodide: "npm:0.28.2"
+    pyodide: "npm:0.29.0"
     react: "npm:^18.2.0"
     typescript: "npm:^5.9.2"
     typescript-eslint: "npm:^8.46.2"
@@ -6996,6 +6996,13 @@ __metadata:
   languageName: node
   linkType: hard
 
+"@types/emscripten@npm:^1.41.4":
+  version: 1.41.5
+  resolution: "@types/emscripten@npm:1.41.5"
+  checksum: 10c0/ae816da716f896434e59df7a71b67c71ae7e85ca067a32aef1616572fc4757459515d42ade6f5b8fd8d69733a9dbd0cf23010fec5b2f41ce52c09501aa350e45
+  languageName: node
+  linkType: hard
+
 "@types/eslint-plugin-jsx-a11y@npm:~6.10.0":
   version: 6.10.1
   resolution: "@types/eslint-plugin-jsx-a11y@npm:6.10.1"
@@ -20739,12 +20746,13 @@ __metadata:
   languageName: node
   linkType: hard
 
-"pyodide@npm:0.28.2":
-  version: 0.28.2
-  resolution: "pyodide@npm:0.28.2"
+"pyodide@npm:0.29.0":
+  version: 0.29.0
+  resolution: "pyodide@npm:0.29.0"
   dependencies:
+    "@types/emscripten": "npm:^1.41.4"
     ws: "npm:^8.5.0"
-  checksum: 10c0/751260ca329ee45665ed61c77f5ad278d8f17248e57a0a560171ed77a238286eec0bfa4ab96993dbc052f3ae9fa0126b4fda96f608cace35de1a2976d4199b26
+  checksum: 10c0/c24c22e4c9f6da78813705b066e9dc2b39e70d2014ff3fe5a9fa14077cdb843f741bb5302c30f60fd043c5873bb808b6abe7cd5508f5b3699067d858c7ee81d8
   languageName: node
   linkType: hard