diff --git a/cmake/check_link_atomic.cmake b/cmake/check_link_atomic.cmake
index d462191a0..aef5cd63f 100644
--- a/cmake/check_link_atomic.cmake
+++ b/cmake/check_link_atomic.cmake
@@ -1,3 +1,8 @@
+if (EMSCRIPTEN OR Z3_SINGLE_THREADED)
+  # Emscripten (Pyodide/WASM) and single-threaded builds do not use
+  # libatomic; skip the check to avoid a spurious configure failure.
+  message(STATUS "Skipping std::atomic link check (EMSCRIPTEN or Z3_SINGLE_THREADED)")
+else()
 set(ATOMIC_TEST_SOURCE "
 #include <atomic>
 std::atomic<int> x;
@@ -21,3 +26,4 @@ if (NOT BUILTIN_ATOMIC)
     message(FATAL_ERROR "Host compiler must support std::atomic!")
   endif()
 endif()
+endif()