diff --git a/clang-tools-extra/clang-tidy/ClangTidyOptions.cpp b/clang-tools-extra/clang-tidy/ClangTidyOptions.cpp
--- a/clang-tools-extra/clang-tidy/ClangTidyOptions.cpp
+++ b/clang-tools-extra/clang-tidy/ClangTidyOptions.cpp
@@ -172,6 +172,7 @@
     IO.mapOptional("ExtraArgsBefore", Options.ExtraArgsBefore);
     IO.mapOptional("InheritParentConfig", Options.InheritParentConfig);
     IO.mapOptional("UseColor", Options.UseColor);
+    IO.mapOptional("SystemHeaders", Options.SystemHeaders);
   }
 };
 
diff --git a/clang-tools-extra/docs/ReleaseNotes.rst b/clang-tools-extra/docs/ReleaseNotes.rst
--- a/clang-tools-extra/docs/ReleaseNotes.rst
+++ b/clang-tools-extra/docs/ReleaseNotes.rst
@@ -103,6 +103,9 @@
 
 - Fix a potential crash when using the `--dump-config` option.
 
+- Support specifying `SystemHeaders` in the `.clang-tidy` configuration file,
+  with the same functionality as the command-line option `--system-headers`.
+
 New checks
 ^^^^^^^^^^
 
diff --git a/clang-tools-extra/test/clang-tidy/infrastructure/Inputs/system-headers/system_header.h b/clang-tools-extra/test/clang-tidy/infrastructure/Inputs/system-headers/system_header.h
new file mode 100644
--- /dev/null
+++ b/clang-tools-extra/test/clang-tidy/infrastructure/Inputs/system-headers/system_header.h
@@ -0,0 +1 @@
+class Foo { Foo(int); };
diff --git a/clang-tools-extra/test/clang-tidy/infrastructure/system-headers.cpp b/clang-tools-extra/test/clang-tidy/infrastructure/system-headers.cpp
new file mode 100644
--- /dev/null
+++ b/clang-tools-extra/test/clang-tidy/infrastructure/system-headers.cpp
@@ -0,0 +1,18 @@
+// RUN: clang-tidy -dump-config -system-headers=true | FileCheck -check-prefix=CHECK-CONFIG-SYSTEM-HEADERS %s
+// RUN: clang-tidy -dump-config -system-headers=false | FileCheck -check-prefix=CHECK-CONFIG-NO-SYSTEM-HEADERS %s
+// RUN: clang-tidy -config='SystemHeaders: true' -dump-config | FileCheck -check-prefix=CHECK-CONFIG-SYSTEM-HEADERS %s
+// RUN: clang-tidy -config='SystemHeaders: false' -dump-config | FileCheck -check-prefix=CHECK-CONFIG-NO-SYSTEM-HEADERS %s
+// RUN: clang-tidy -help | FileCheck -check-prefix=CHECK-OPT-PRESENT %s
+
+// RUN: clang-tidy -checks='-*,google-explicit-constructor' -header-filter='.*' -system-headers=true %s -- -isystem %S/Inputs/system-headers 2>&1 | FileCheck -check-prefix=CHECK-SYSTEM-HEADERS %s
+// RUN: clang-tidy -checks='-*,google-explicit-constructor' -header-filter='.*' -system-headers=false %s -- -isystem %S/Inputs/system-headers 2>&1 | FileCheck -check-prefix=CHECK-NO-SYSTEM-HEADERS %s
+// RUN: clang-tidy -checks='-*,google-explicit-constructor' -header-filter='.*' -config='SystemHeaders: true' %s -- -isystem %S/Inputs/system-headers 2>&1 | FileCheck -check-prefix=CHECK-SYSTEM-HEADERS %s
+// RUN: clang-tidy -checks='-*,google-explicit-constructor' -header-filter='.*' -config='SystemHeaders: false' %s -- -isystem %S/Inputs/system-headers 2>&1 | FileCheck -check-prefix=CHECK-NO-SYSTEM-HEADERS %s
+
+#include <system_header.h>
+// CHECK-SYSTEM-HEADERS: system_header.h:1:13: warning: single-argument constructors must be marked explicit
+// CHECK-NO-SYSTEM-HEADERS-NOT: system_header.h:1:13: warning: single-argument constructors must be marked explicit
+
+// CHECK-CONFIG-NO-SYSTEM-HEADERS: SystemHeaders: false
+// CHECK-CONFIG-SYSTEM-HEADERS: SystemHeaders: true
+// CHECK-OPT-PRESENT: --system-headers
diff --git a/clang-tools-extra/unittests/clang-tidy/ClangTidyOptionsTest.cpp b/clang-tools-extra/unittests/clang-tidy/ClangTidyOptionsTest.cpp
--- a/clang-tools-extra/unittests/clang-tidy/ClangTidyOptionsTest.cpp
+++ b/clang-tools-extra/unittests/clang-tidy/ClangTidyOptionsTest.cpp
@@ -120,6 +120,7 @@
       ExtraArgs: ['arg1', 'arg2']
       ExtraArgsBefore: ['arg-before1', 'arg-before2']
       UseColor: false
+      SystemHeaders: false
   )",
                                                "Options1"));
   ASSERT_TRUE(!!Options1);
@@ -134,6 +135,7 @@
       ExtraArgs: ['arg3', 'arg4']
       ExtraArgsBefore: ['arg-before3', 'arg-before4']
       UseColor: true
+      SystemHeaders: true
   )",
                                                "Options2"));
   ASSERT_TRUE(!!Options2);
@@ -154,6 +156,9 @@
                        Options.ExtraArgsBefore->end(), ","));
   ASSERT_TRUE(Options.UseColor.has_value());
   EXPECT_TRUE(*Options.UseColor);
+
+  ASSERT_TRUE(Options.SystemHeaders.has_value());
+  EXPECT_TRUE(*Options.SystemHeaders);
 }
 
 namespace {
@@ -249,6 +254,17 @@
                                          DiagKind(llvm::SourceMgr::DK_Error),
                                          DiagPos(Options.range().Begin),
                                          DiagRange(Options.range()))));
+
+  Options = llvm::Annotations(R"(
+    SystemHeaders: [[NotABool]]
+  )");
+  ParsedOpt = ParseWithDiags(Options.code());
+  EXPECT_TRUE(!ParsedOpt);
+  EXPECT_THAT(Collector.getDiags(),
+              testing::ElementsAre(AllOf(DiagMessage("invalid boolean"),
+                                         DiagKind(llvm::SourceMgr::DK_Error),
+                                         DiagPos(Options.range().Begin),
+                                         DiagRange(Options.range()))));
 }
 
 namespace {