diff --git a/src/plugins/clangcodemodel/clangutils.cpp b/src/plugins/clangcodemodel/clangutils.cpp
index b58304eb2b4..8f11758ac4d 100644
--- a/src/plugins/clangcodemodel/clangutils.cpp
+++ b/src/plugins/clangcodemodel/clangutils.cpp
@@ -153,9 +153,9 @@ private:
 
         if (m_projectPart.qtVersion != CppTools::ProjectPart::NoQt) {
             const QString wrappedQtCoreHeaderPath = wrappedQtHeadersPath + "/QtCore";
-            add(includeDirOption());
+            add(includeDirOptionForPath(wrappedQtHeadersPath));
             add(QDir::toNativeSeparators(wrappedQtHeadersPath));
-            add(includeDirOption());
+            add(includeDirOptionForPath(wrappedQtHeadersPath));
             add(QDir::toNativeSeparators(wrappedQtCoreHeaderPath));
         }
     }
@@ -164,7 +164,7 @@ private:
     {
         const QString path = ModelManagerSupportClang::instance()->dummyUiHeaderOnDiskDirPath();
         if (!path.isEmpty()) {
-            add(includeDirOption());
+            add("-I");
             add(QDir::toNativeSeparators(path));
         }
     }
diff --git a/src/plugins/clangpchmanager/projectupdater.cpp b/src/plugins/clangpchmanager/projectupdater.cpp
index 66c63d1387b..ce890ee1174 100644
--- a/src/plugins/clangpchmanager/projectupdater.cpp
+++ b/src/plugins/clangpchmanager/projectupdater.cpp
@@ -149,7 +149,7 @@ HeaderAndSources ProjectUpdater::headerAndSourcesFromProjectPart(
 QStringList ProjectUpdater::compilerArguments(CppTools::ProjectPart *projectPart)
 {
     using CppTools::CompilerOptionsBuilder;
-    CompilerOptionsBuilder builder(*projectPart);
+    CompilerOptionsBuilder builder(*projectPart, CppTools::UseSystemHeader::Yes);
     return builder.build(CppTools::ProjectFile::CXXHeader, CompilerOptionsBuilder::PchUsage::None);
 }
 
diff --git a/src/plugins/clangrefactoring/clangqueryprojectsfindfilter.cpp b/src/plugins/clangrefactoring/clangqueryprojectsfindfilter.cpp
index 336a681ab2a..77d4a9ef6e2 100644
--- a/src/plugins/clangrefactoring/clangqueryprojectsfindfilter.cpp
+++ b/src/plugins/clangrefactoring/clangqueryprojectsfindfilter.cpp
@@ -153,7 +153,7 @@ Utils::SmallStringVector ClangQueryProjectsFindFilter::compilerArguments(CppTool
 {
     using CppTools::CompilerOptionsBuilder;
 
-    CompilerOptionsBuilder builder(*projectPart);
+    CompilerOptionsBuilder builder(*projectPart, CppTools::UseSystemHeader::Yes);
 
     return Utils::SmallStringVector(builder.build(fileKind,
                                                   CompilerOptionsBuilder::PchUsage::None));
diff --git a/src/plugins/clangrefactoring/refactoringengine.cpp b/src/plugins/clangrefactoring/refactoringengine.cpp
index b5127e2b88f..57122fd3bea 100644
--- a/src/plugins/clangrefactoring/refactoringengine.cpp
+++ b/src/plugins/clangrefactoring/refactoringengine.cpp
@@ -74,7 +74,7 @@ void RefactoringEngine::startLocalRenaming(const CppTools::CursorInEditor &data,
 
     QString filePath = data.filePath().toString();
     QTextCursor textCursor = data.cursor();
-    CompilerOptionsBuilder optionsBuilder{*projectPart};
+    CompilerOptionsBuilder optionsBuilder{*projectPart, CppTools::UseSystemHeader::Yes};
     Utils::SmallStringVector commandLine{optionsBuilder.build(
                     fileKindInProjectPart(projectPart, filePath),
                     CppTools::getPchUsage())};
diff --git a/src/plugins/cpptools/compileroptionsbuilder.cpp b/src/plugins/cpptools/compileroptionsbuilder.cpp
index 041cbf607b2..aeb60a0f282 100644
--- a/src/plugins/cpptools/compileroptionsbuilder.cpp
+++ b/src/plugins/cpptools/compileroptionsbuilder.cpp
@@ -29,6 +29,7 @@
 #include <coreplugin/vcsmanager.h>
 
 #include <projectexplorer/projectexplorerconstants.h>
+#include <projectexplorer/project.h>
 
 #include <utils/fileutils.h>
 #include <utils/qtcassert.h>
@@ -38,8 +39,10 @@
 
 namespace CppTools {
 
-CompilerOptionsBuilder::CompilerOptionsBuilder(const ProjectPart &projectPart)
-    : m_projectPart(projectPart)
+CompilerOptionsBuilder::CompilerOptionsBuilder(const ProjectPart &projectPart,
+                                               UseSystemHeader useSystemHeader)
+    : m_projectPart(projectPart),
+      m_useSystemHeader(useSystemHeader)
 {
 }
 
@@ -188,7 +191,6 @@ void CompilerOptionsBuilder::enableExceptions()
 void CompilerOptionsBuilder::addHeaderPathOptions()
 {
     typedef ProjectPartHeaderPath HeaderPath;
-    const QString defaultPrefix = includeDirOption();
 
     QStringList result;
 
@@ -208,7 +210,7 @@ void CompilerOptionsBuilder::addHeaderPathOptions()
         default: // This shouldn't happen, but let's be nice..:
             // intentional fall-through:
         case HeaderPath::IncludePath:
-            prefix = defaultPrefix;
+            prefix = includeDirOptionForPath(headerPath.path);
             break;
         }
 
@@ -423,9 +425,14 @@ void CompilerOptionsBuilder::addDefineFunctionMacrosMsvc()
         addMacros({{"__FUNCSIG__", "\"\""}, {"__FUNCTION__", "\"\""}, {"__FUNCDNAME__", "\"\""}});
 }
 
-QString CompilerOptionsBuilder::includeDirOption() const
+QString CompilerOptionsBuilder::includeDirOptionForPath(const QString &path) const
 {
-    return QLatin1String("-I");
+    if (m_useSystemHeader == UseSystemHeader::No
+            || path.startsWith(m_projectPart.project->rootProjectDirectory().toString())) {
+        return QString("-I");
+    } else {
+        return QString("-isystem");
+    }
 }
 
 QByteArray CompilerOptionsBuilder::macroOption(const ProjectExplorer::Macro &macro) const
diff --git a/src/plugins/cpptools/compileroptionsbuilder.h b/src/plugins/cpptools/compileroptionsbuilder.h
index eddbd6d3fb6..75241dd0231 100644
--- a/src/plugins/cpptools/compileroptionsbuilder.h
+++ b/src/plugins/cpptools/compileroptionsbuilder.h
@@ -31,6 +31,12 @@
 
 namespace CppTools {
 
+enum class UseSystemHeader
+{
+    Yes,
+    No
+};
+
 class CPPTOOLS_EXPORT CompilerOptionsBuilder
 {
 public:
@@ -39,7 +45,8 @@ public:
         Use
     };
 
-    CompilerOptionsBuilder(const ProjectPart &projectPart);
+    CompilerOptionsBuilder(const ProjectPart &projectPart,
+                           UseSystemHeader useSystemHeader = UseSystemHeader::No);
     virtual ~CompilerOptionsBuilder() {}
 
     virtual void addTargetTriple();
@@ -80,8 +87,7 @@ protected:
     virtual QString defineOption() const;
     virtual QString undefineOption() const;
     virtual QString includeOption() const;
-    virtual QString includeDirOption() const;
-
+    QString includeDirOptionForPath(const QString &path) const;
     const ProjectPart m_projectPart;
 
 private:
@@ -90,6 +96,7 @@ private:
     QString defineDirectiveToDefineOption(const ProjectExplorer::Macro &marco) const;
 
     QStringList m_options;
+    UseSystemHeader m_useSystemHeader;
 };
 
 } // namespace CppTools
diff --git a/src/plugins/projectexplorer/project.cpp b/src/plugins/projectexplorer/project.cpp
index 803dd3be672..43188661dfa 100644
--- a/src/plugins/projectexplorer/project.cpp
+++ b/src/plugins/projectexplorer/project.cpp
@@ -642,6 +642,15 @@ Utils::FileName Project::projectDirectory(const Utils::FileName &top)
     return Utils::FileName::fromString(top.toFileInfo().absoluteDir().path());
 }
 
+/*!
+    Returns the common root directory that contains all files which belongs to a project.
+*/
+
+Utils::FileName Project::rootProjectDirectory() const
+{
+    return projectDirectory(); // TODO parse all files and find the common path
+}
+
 ProjectNode *Project::rootProjectNode() const
 {
     return d->m_rootProjectNode.get();
diff --git a/tests/unit/mockup/projectexplorer/project.h b/tests/unit/mockup/projectexplorer/project.h
index ea040fbc490..78b4211dca4 100644
--- a/tests/unit/mockup/projectexplorer/project.h
+++ b/tests/unit/mockup/projectexplorer/project.h
@@ -36,6 +36,10 @@ public:
     Utils::FileName projectDirectory() const {
         return Utils::FileName();
     }
+
+    Utils::FileName rootProjectDirectory() const {
+        return Utils::FileName();
+    }
 };
 
 }