diff --git a/clang-tools-extra/clangd/IncludeCleaner.cpp b/clang-tools-extra/clangd/IncludeCleaner.cpp
--- a/clang-tools-extra/clangd/IncludeCleaner.cpp
+++ b/clang-tools-extra/clangd/IncludeCleaner.cpp
@@ -71,6 +71,8 @@
 bool mayConsiderUnused(
     const Inclusion &Inc, ParsedAST &AST,
     const include_cleaner::PragmaIncludes *PI) {
+  if (PI && PI->shouldKeep(Inc.HashLine + 1))
+      return false;
   // FIXME(kirillbobyrev): We currently do not support the umbrella headers.
   // System headers are likely to be standard library headers.
   // Until we have good support for umbrella headers, don't warn about them.
@@ -82,8 +84,6 @@
       AST.getIncludeStructure().getRealPath(HID));
   assert(FE);
   if (PI) {
-    if (PI->shouldKeep(Inc.HashLine + 1))
-      return false;
     // Check if main file is the public interface for a private header. If so we
     // shouldn't diagnose it as unused.
     if (auto PHeader = PI->getPublic(*FE); !PHeader.empty()) {
diff --git a/clang-tools-extra/clangd/unittests/IncludeCleanerTests.cpp b/clang-tools-extra/clangd/unittests/IncludeCleanerTests.cpp
--- a/clang-tools-extra/clangd/unittests/IncludeCleanerTests.cpp
+++ b/clang-tools-extra/clangd/unittests/IncludeCleanerTests.cpp
@@ -78,6 +78,8 @@
   auto TU = TestTU::withCode(R"cpp(
     #include <list>
     #include <queue>
+    #include <vector> // IWYU pragma: keep
+    #include <string> // IWYU pragma: export
     std::list<int> x;
   )cpp");
   // Layout of std library impl is not relevant.
@@ -86,10 +88,13 @@
     namespace std {
       template <typename> class list {};
       template <typename> class queue {};
+      template <typename> class vector {};
     }
   )cpp";
   TU.AdditionalFiles["list"] = "#include <bits>";
   TU.AdditionalFiles["queue"] = "#include <bits>";
+  TU.AdditionalFiles["vector"] = "#include <bits>";
+  TU.AdditionalFiles["string"] = "#include <bits>";
   TU.ExtraArgs = {"-isystem", testRoot()};
   auto AST = TU.build();
   IncludeCleanerFindings Findings = computeIncludeCleanerFindings(AST);