diff --git a/clang/lib/Lex/DependencyDirectivesSourceMinimizer.cpp b/clang/lib/Lex/DependencyDirectivesSourceMinimizer.cpp
--- a/clang/lib/Lex/DependencyDirectivesSourceMinimizer.cpp
+++ b/clang/lib/Lex/DependencyDirectivesSourceMinimizer.cpp
@@ -763,12 +763,11 @@
   if (top() == pp_else)
     popToken();
 
-  // Strip out "#elif" if they're empty.
-  while (top() == pp_elif)
-    popToken();
-
-  // If "#if" is empty, strip it and skip the "#endif".
-  if (top() == pp_if || top() == pp_ifdef || top() == pp_ifndef) {
+  // If "#ifdef" is empty, strip it and skip the "#endif".
+  // Avoid stripping "#if" / "#elif" as they could contain a "__has_include"
+  // (either directly, or through a macro expansion) without an "#include"
+  // inside the "#if/elif", which could affect the dependency output.
+  if (top() == pp_ifdef || top() == pp_ifndef) {
     popToken();
     skipLine(First, End);
     return false;
diff --git a/clang/test/ClangScanDeps/Inputs/has_include_if_elif.json b/clang/test/ClangScanDeps/Inputs/has_include_if_elif.json
new file mode 100644
--- /dev/null
+++ b/clang/test/ClangScanDeps/Inputs/has_include_if_elif.json
@@ -0,0 +1,7 @@
+[
+{
+  "directory": "DIR",
+  "command": "clang -E DIR/has_include_if_elif2.cpp -IInputs",
+  "file": "DIR/has_include_if_elif2.cpp"
+}
+]
diff --git a/clang/test/ClangScanDeps/has_include_if_elif.cpp b/clang/test/ClangScanDeps/has_include_if_elif.cpp
new file mode 100644
--- /dev/null
+++ b/clang/test/ClangScanDeps/has_include_if_elif.cpp
@@ -0,0 +1,38 @@
+// RUN: rm -rf %t.dir
+// RUN: rm -rf %t.cdb
+// RUN: mkdir -p %t.dir
+// RUN: cp %s %t.dir/has_include_if_elif2.cpp
+// RUN: mkdir %t.dir/Inputs
+// RUN: cp %S/Inputs/header.h %t.dir/Inputs/header.h
+// RUN: cp %S/Inputs/header.h %t.dir/Inputs/header2.h
+// RUN: cp %S/Inputs/header.h %t.dir/Inputs/header3.h
+// RUN: cp %S/Inputs/header.h %t.dir/Inputs/header4.h
+// RUN: sed -e "s|DIR|%/t.dir|g" %S/Inputs/has_include_if_elif.json > %t.cdb
+//
+// RUN: clang-scan-deps -compilation-database %t.cdb -j 1 -mode preprocess-minimized-sources | \
+// RUN:   FileCheck %s
+// RUN: clang-scan-deps -compilation-database %t.cdb -j 1 -mode preprocess | \
+// RUN:   FileCheck %s
+
+#if __has_include("header.h")
+#endif
+
+#if 0
+#elif __has_include("header2.h")
+#endif
+
+#define H3 __has_include("header3.h")
+#if H3
+#endif
+
+#define H4 __has_include("header4.h")
+
+#if 0
+#elif H4
+#endif
+
+// CHECK: has_include_if_elif2.cpp
+// CHECK-NEXT: Inputs{{/|\\}}header.h
+// CHECK-NEXT: Inputs{{/|\\}}header2.h
+// CHECK-NEXT: Inputs{{/|\\}}header3.h
+// CHECK-NEXT: Inputs{{/|\\}}header4.h
diff --git a/clang/unittests/Lex/DependencyDirectivesSourceMinimizerTest.cpp b/clang/unittests/Lex/DependencyDirectivesSourceMinimizerTest.cpp
--- a/clang/unittests/Lex/DependencyDirectivesSourceMinimizerTest.cpp
+++ b/clang/unittests/Lex/DependencyDirectivesSourceMinimizerTest.cpp
@@ -328,12 +328,17 @@
   SmallVector<char, 128> Out;
 
   ASSERT_FALSE(minimizeSourceToDependencyDirectives("#ifdef A\n"
+                                                    "void skip();\n"
                                                     "#elif B\n"
                                                     "#elif C\n"
                                                     "#else D\n"
                                                     "#endif\n",
                                                     Out));
-  EXPECT_STREQ("", Out.data());
+  EXPECT_STREQ("#ifdef A\n"
+               "#elif B\n"
+               "#elif C\n"
+               "#endif\n",
+               Out.data());
 }
 
 TEST(MinimizeSourceToDependencyDirectivesTest, Pragma) {
@@ -507,6 +512,12 @@
   for (auto Source : {
            "#warning \\\n#include <t.h>\n",
            "#error \\\n#include <t.h>\n",
+       }) {
+    ASSERT_FALSE(minimizeSourceToDependencyDirectives(Source, Out));
+    EXPECT_STREQ("", Out.data());
+  }
+
+  for (auto Source : {
            "#if MACRO\n#warning '\n#endif\n",
            "#if MACRO\n#warning \"\n#endif\n",
            "#if MACRO\n#warning /*\n#endif\n",
@@ -515,7 +526,7 @@
            "#if MACRO\n#error /*\n#endif\n",
        }) {
     ASSERT_FALSE(minimizeSourceToDependencyDirectives(Source, Out));
-    EXPECT_STREQ("", Out.data());
+    EXPECT_STREQ("#if MACRO\n#endif\n", Out.data());
   }
 }
 
@@ -543,7 +554,7 @@
 #include <test.h>
 )";
   ASSERT_FALSE(minimizeSourceToDependencyDirectives(Source, Out));
-  EXPECT_STREQ("#include <test.h>\n", Out.data());
+  EXPECT_STREQ("#if DEBUG\n#endif\n#include <test.h>\n", Out.data());
 }
 
 TEST(MinimizeSourceToDependencyDirectivesTest, CharacterLiteralPrefixU) {