diff --git a/src/plugins/cpptools/compileroptionsbuilder.cpp b/src/plugins/cpptools/compileroptionsbuilder.cpp
index e5685dc5e05..f757f2fe2cc 100644
--- a/src/plugins/cpptools/compileroptionsbuilder.cpp
+++ b/src/plugins/cpptools/compileroptionsbuilder.cpp
@@ -741,6 +741,15 @@ void CompilerOptionsBuilder::evaluateCompilerFlags()
             continue;
         }
 
+        if (option.startsWith("/Y", Qt::CaseSensitive)
+            || (option.startsWith("/F", Qt::CaseSensitive) && option != "/F")) {
+            // Precompiled header flags.
+            // Skip also the next option if it's not glued to the current one.
+            if (option.size() > 3)
+                skipNext = true;
+            continue;
+        }
+
         // Check whether a language version is already used.
         QString theOption = option;
         if (theOption.startsWith("-std=")) {
diff --git a/src/plugins/projectexplorer/msvctoolchain.cpp b/src/plugins/projectexplorer/msvctoolchain.cpp
index 8b8c5711428..9c86a706869 100644
--- a/src/plugins/projectexplorer/msvctoolchain.cpp
+++ b/src/plugins/projectexplorer/msvctoolchain.cpp
@@ -1027,6 +1027,8 @@ bool static hasFlagEffectOnMacros(const QString &flag)
             return false; // Skip include paths
         if (f.startsWith("w", Qt::CaseInsensitive))
             return false; // Skip warning options
+        if (f.startsWith("Y") || (f.startsWith("F") && f != "F"))
+            return false; // Skip pch-related flags
     }
     return true;
 }