diff --git a/src/bootstrap/native.rs b/src/bootstrap/native.rs
index 48b2cc24d4c..e1e14893b9a 100644
--- a/src/bootstrap/native.rs
+++ b/src/bootstrap/native.rs
@@ -282,14 +282,6 @@ impl Step for Llvm {
                 "LLVM_CONFIG_PATH",
                 host_bin.join("llvm-config").with_extension(EXE_EXTENSION),
             );
-
-            if target.contains("netbsd") {
-                cfg.define("CMAKE_SYSTEM_NAME", "NetBSD");
-            } else if target.contains("freebsd") {
-                cfg.define("CMAKE_SYSTEM_NAME", "FreeBSD");
-            } else if target.contains("windows") {
-                cfg.define("CMAKE_SYSTEM_NAME", "Windows");
-            }
         }
 
         if let Some(ref suffix) = builder.config.llvm_version_suffix {
@@ -378,6 +370,22 @@ fn configure_cmake(
     }
     cfg.target(&target.triple).host(&builder.config.build.triple);
 
+    if target != builder.config.build {
+        if target.contains("netbsd") {
+            cfg.define("CMAKE_SYSTEM_NAME", "NetBSD");
+        } else if target.contains("freebsd") {
+            cfg.define("CMAKE_SYSTEM_NAME", "FreeBSD");
+        } else if target.contains("windows") {
+            cfg.define("CMAKE_SYSTEM_NAME", "Windows");
+        }
+        // When cross-compiling we should also set CMAKE_SYSTEM_VERSION, but in
+        // that case like CMake we cannot easily determine system version either.
+        //
+        // Since, the LLVM itself makes rather limited use of version checks in
+        // CMakeFiles (and then only in tests), and so far no issues have been
+        // reported, the system version is currently left unset.
+    }
+
     let sanitize_cc = |cc: &Path| {
         if target.contains("msvc") {
             OsString::from(cc.to_str().unwrap().replace("\\", "/"))