diff --git a/src/missing_deps.cc b/src/missing_deps.cc
index a0fd048..adce2d2 100644
--- a/src/missing_deps.cc
+++ b/src/missing_deps.cc
@@ -114,6 +114,14 @@
   std::set<Edge*> deplog_edges;
   for (int i = 0; i < dep_nodes_count; ++i) {
     Node* deplog_node = dep_nodes[i];
+    // Special exception: A dep on build.ninja can be used to mean "always
+    // rebuild this target when the build is reconfigured", but build.ninja is
+    // often generated by a configuration tool like cmake or gn. The rest of
+    // the build "implicitly" depends on the entire build being reconfigured,
+    // so a missing dep path to build.ninja is not an actual missing dependecy
+    // problem.
+    if (deplog_node->path() == "build.ninja")
+      return;
     Edge* deplog_edge = deplog_node->in_edge();
     if (deplog_edge) {
       deplog_edges.insert(deplog_edge);