diff --git a/pkg/nanopb/Makefile b/pkg/nanopb/Makefile
index 422a5abc79..7ee55de18d 100644
--- a/pkg/nanopb/Makefile
+++ b/pkg/nanopb/Makefile
@@ -1,6 +1,6 @@
 PKG_NAME=nanopb
 PKG_URL=https://github.com/nanopb/nanopb
-PKG_VERSION=493adf3616bee052649c63c473f8355630c2797f # nanopb-0.3.9.4
+PKG_VERSION=3eb9a75c1e66e6182e87e2bd758ff2a4d16acbdc # nanopb-0.4.1
 PKG_LICENSE=MIT
 
 include $(RIOTBASE)/pkg/pkg.mk
diff --git a/pkg/nanopb/patches/0001-generator-nanopb_generator.py-use-python3.patch b/pkg/nanopb/patches/0001-generator-nanopb_generator.py-use-python3.patch
index d8ed6a5343..db6b4f63d3 100644
Binary files a/pkg/nanopb/patches/0001-generator-nanopb_generator.py-use-python3.patch and b/pkg/nanopb/patches/0001-generator-nanopb_generator.py-use-python3.patch differ