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
@@ -223,7 +223,7 @@
   // headers are likely to be the Standard Library headers. Until we have a
   // good support for umbrella headers and Standard Library headers, don't warn
   // about them.
-  if (Inc.Written.front() == '<')
+  if (Inc.Written.front() == '<' || Inc.BehindPragmaKeep)
     return false;
   // Headers without include guards have side effects and are not
   // self-contained, skip them.
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
@@ -397,6 +397,25 @@
               UnorderedElementsAre(testPath("foo.h")));
 }
 
+TEST(IncludeCleaner, IWYUPragmas) {
+  TestTU TU;
+  TU.Code = R"cpp(
+    #include "behind_keep.h" // IWYU pragma: keep
+    )cpp";
+  TU.AdditionalFiles["behind_keep.h"] = guard("");
+  ParsedAST AST = TU.build();
+
+  auto ReferencedFiles =
+      findReferencedFiles(findReferencedLocations(AST),
+                          AST.getIncludeStructure(), AST.getSourceManager());
+  llvm::StringSet<> ReferencedFileNames;
+  EXPECT_TRUE(ReferencedFiles.empty());
+  auto &Includes = AST.getIncludeStructure();
+  EXPECT_THAT(getUnused(AST, translateToHeaderIDs(ReferencedFiles, Includes,
+                                                  AST.getSourceManager())),
+              ::testing::IsEmpty());
+}
+
 } // namespace
 } // namespace clangd
 } // namespace clang