diff --git a/Makefile b/Makefile
index f9efb64bcf3d..5e67e4888f58 100644
--- a/Makefile
+++ b/Makefile
@@ -1094,7 +1094,8 @@ RUNTIME_CXX_FLAGS = \
     -Wno-unknown-warning-option \
     -Wno-unused-function \
     -Wvla \
-    -Wsign-compare
+    -Wsign-compare \
+    -Wno-sync-alignment
 
 $(BUILD_DIR)/initmod.windows_%_x86_32.ll: $(SRC_DIR)/runtime/windows_%_x86.cpp $(BUILD_DIR)/clang_ok
 	@mkdir -p $(@D)
diff --git a/src/runtime/CMakeLists.txt b/src/runtime/CMakeLists.txt
index 48f946b00de9..c76c482e07ad 100644
--- a/src/runtime/CMakeLists.txt
+++ b/src/runtime/CMakeLists.txt
@@ -173,6 +173,7 @@ set(RUNTIME_CXX_FLAGS
     -Wvla
     -Wsign-compare
     -Wimplicit-fallthrough
+    -Wno-sync-alignment
 )
 
 option(Halide_CLANG_TIDY_BUILD "Generate fake compile jobs for runtime files when running clang-tidy." OFF)