diff --git a/Framework/PythonInterface/mantid/api/src/Exports/Algorithm.cpp b/Framework/PythonInterface/mantid/api/src/Exports/Algorithm.cpp
index 2498440c98530999e3d64a21f0e56c2c5b7e7484..843ccf1e8b1eaa9ca3ad952c8f491d400455e074 100644
--- a/Framework/PythonInterface/mantid/api/src/Exports/Algorithm.cpp
+++ b/Framework/PythonInterface/mantid/api/src/Exports/Algorithm.cpp
@@ -44,6 +44,7 @@ typedef void (*declarePropertyType4)(boost::python::object &self,
                                      const boost::python::object &, const int);
 #ifdef __clang__
 #pragma clang diagnostic push
+#pragma clang diagnostic ignored "-Wunknown-pragmas"
 #pragma clang diagnostic ignored "-Wunused-local-typedef"
 #endif
 // Overload types
diff --git a/Framework/PythonInterface/mantid/api/src/Exports/AlgorithmFactory.cpp b/Framework/PythonInterface/mantid/api/src/Exports/AlgorithmFactory.cpp
index 9a8b9a56ecc0b2af10f9ef3e8ba93f31671d0245..14fa42684ddb16434842304533d8508d63033ff7 100644
--- a/Framework/PythonInterface/mantid/api/src/Exports/AlgorithmFactory.cpp
+++ b/Framework/PythonInterface/mantid/api/src/Exports/AlgorithmFactory.cpp
@@ -101,6 +101,7 @@ void subscribe(AlgorithmFactoryImpl &self, const boost::python::object &obj) {
 }
 #ifdef __clang__
 #pragma clang diagnostic push
+#pragma clang diagnostic ignored "-Wunknown-pragmas"
 #pragma clang diagnostic ignored "-Wunused-local-typedef"
 #endif
 BOOST_PYTHON_MEMBER_FUNCTION_OVERLOADS(existsOverloader, exists, 1, 2)
diff --git a/Framework/PythonInterface/mantid/api/src/Exports/AlgorithmManager.cpp b/Framework/PythonInterface/mantid/api/src/Exports/AlgorithmManager.cpp
index a280b6b4f18e08d60a7b3951804e8b0800c57a17..15aa52abed074a2c1c67e30a011043c131cc01a6 100644
--- a/Framework/PythonInterface/mantid/api/src/Exports/AlgorithmManager.cpp
+++ b/Framework/PythonInterface/mantid/api/src/Exports/AlgorithmManager.cpp
@@ -59,6 +59,7 @@ boost::python::list runningInstancesOf(AlgorithmManagerImpl &self,
 //------------------------------------------------------------------------------------------------------
 #ifdef __clang__
 #pragma clang diagnostic push
+#pragma clang diagnostic ignored "-Wunknown-pragmas"
 #pragma clang diagnostic ignored "-Wunused-local-typedef"
 #endif
 /// Define overload generators
diff --git a/Framework/PythonInterface/mantid/api/src/Exports/Axis.cpp b/Framework/PythonInterface/mantid/api/src/Exports/Axis.cpp
index 131d361928396e4bc186d79d14fb0c04a93530fb..134ea0eecfdb293583ce9e7ef8a67dbb8de7479b 100644
--- a/Framework/PythonInterface/mantid/api/src/Exports/Axis.cpp
+++ b/Framework/PythonInterface/mantid/api/src/Exports/Axis.cpp
@@ -27,6 +27,7 @@ namespace bpl = boost::python;
 //------------------------------- Overload macros ---------------------------
 #ifdef __clang__
 #pragma clang diagnostic push
+#pragma clang diagnostic ignored "-Wunknown-pragmas"
 #pragma clang diagnostic ignored "-Wunused-local-typedef"
 #endif
 
diff --git a/Framework/PythonInterface/mantid/api/src/Exports/ExperimentInfo.cpp b/Framework/PythonInterface/mantid/api/src/Exports/ExperimentInfo.cpp
index db5e854e4d1d9275cca4b98d0360f32d20dd5fa8..926a6d0b31e49e4e9970553c29118e819f30f7fd 100644
--- a/Framework/PythonInterface/mantid/api/src/Exports/ExperimentInfo.cpp
+++ b/Framework/PythonInterface/mantid/api/src/Exports/ExperimentInfo.cpp
@@ -12,6 +12,7 @@ using namespace boost::python;
 
 #ifdef __clang__
 #pragma clang diagnostic push
+#pragma clang diagnostic ignored "-Wunknown-pragmas"
 #pragma clang diagnostic ignored "-Wunused-local-typedef"
 #endif
 /// Overload generator for getInstrumentFilename
diff --git a/Framework/PythonInterface/mantid/api/src/Exports/FileFinder.cpp b/Framework/PythonInterface/mantid/api/src/Exports/FileFinder.cpp
index 63c0cdea79105dd912ffb126390b997fa00320cb..6f50a63f0d945bc3f01b14f5103a8d42f7b63aaa 100644
--- a/Framework/PythonInterface/mantid/api/src/Exports/FileFinder.cpp
+++ b/Framework/PythonInterface/mantid/api/src/Exports/FileFinder.cpp
@@ -10,6 +10,7 @@ using namespace boost::python;
 namespace {
 #ifdef __clang__
 #pragma clang diagnostic push
+#pragma clang diagnostic ignored "-Wunknown-pragmas"
 #pragma clang diagnostic ignored "-Wunused-local-typedef"
 #endif
 BOOST_PYTHON_MEMBER_FUNCTION_OVERLOADS(getFullPathOverloader, getFullPath, 1, 2)
diff --git a/Framework/PythonInterface/mantid/api/src/Exports/IFunction.cpp b/Framework/PythonInterface/mantid/api/src/Exports/IFunction.cpp
index 1a6a06c4d861d9b0d477ac769d7aa16068b5a0de..c517492f0ac447c26864903f09306b5683a8065a 100644
--- a/Framework/PythonInterface/mantid/api/src/Exports/IFunction.cpp
+++ b/Framework/PythonInterface/mantid/api/src/Exports/IFunction.cpp
@@ -36,6 +36,7 @@ PyObject *getCategories(IFunction &self) {
 typedef void (IFunction::*setParameterType1)(size_t, const double &value, bool);
 #ifdef __clang__
 #pragma clang diagnostic push
+#pragma clang diagnostic ignored "-Wunknown-pragmas"
 #pragma clang diagnostic ignored "-Wunused-local-typedef"
 #endif
 BOOST_PYTHON_MEMBER_FUNCTION_OVERLOADS(setParameterType1_Overloads,
diff --git a/Framework/PythonInterface/mantid/api/src/Exports/MatrixWorkspace.cpp b/Framework/PythonInterface/mantid/api/src/Exports/MatrixWorkspace.cpp
index 95cbce21335fb0df15de7b11662ed94fbf02cf75..7be15fa4d6a0798a2911a6bd218c4a2aa7291b6d 100644
--- a/Framework/PythonInterface/mantid/api/src/Exports/MatrixWorkspace.cpp
+++ b/Framework/PythonInterface/mantid/api/src/Exports/MatrixWorkspace.cpp
@@ -36,6 +36,7 @@ typedef return_value_policy<VectorRefToNumpy<WrapReadWrite>>
 //------------------------------- Overload macros ---------------------------
 #ifdef __clang__
 #pragma clang diagnostic push
+#pragma clang diagnostic ignored "-Wunknown-pragmas"
 #pragma clang diagnostic ignored "-Wunused-local-typedef"
 #endif
 // Overloads for binIndexOf function which has 1 optional argument
diff --git a/Framework/PythonInterface/mantid/api/src/Exports/Workspace.cpp b/Framework/PythonInterface/mantid/api/src/Exports/Workspace.cpp
index 8cd1926d6cdf7039dd9571c29c227bf2039c6c31..e1943cc6a740d1e21760b84822ac78d760d4f4ff 100644
--- a/Framework/PythonInterface/mantid/api/src/Exports/Workspace.cpp
+++ b/Framework/PythonInterface/mantid/api/src/Exports/Workspace.cpp
@@ -16,6 +16,7 @@ namespace {
 ///@cond
 #ifdef __clang__
 #pragma clang diagnostic push
+#pragma clang diagnostic ignored "-Wunknown-pragmas"
 #pragma clang diagnostic ignored "-Wunused-local-typedef"
 #endif
 BOOST_PYTHON_MEMBER_FUNCTION_OVERLOADS(Workspace_isDirtyOverloads,
diff --git a/Framework/PythonInterface/mantid/api/src/Exports/WorkspaceFactory.cpp b/Framework/PythonInterface/mantid/api/src/Exports/WorkspaceFactory.cpp
index 0f1dc2f8e610a9b32cce838829c6b28fd8209f20..0057a3ea6089e7908683974b8db845216dbd06b2 100644
--- a/Framework/PythonInterface/mantid/api/src/Exports/WorkspaceFactory.cpp
+++ b/Framework/PythonInterface/mantid/api/src/Exports/WorkspaceFactory.cpp
@@ -42,6 +42,7 @@ Workspace_sptr createFromParentPtr(WorkspaceFactoryImpl &self,
 /// Overload generator for create
 #ifdef __clang__
 #pragma clang diagnostic push
+#pragma clang diagnostic ignored "-Wunknown-pragmas"
 #pragma clang diagnostic ignored "-Wunused-local-typedef"
 #endif
 BOOST_PYTHON_FUNCTION_OVERLOADS(createFromParent_Overload, createFromParentPtr,
diff --git a/Framework/PythonInterface/mantid/geometry/src/Exports/Component.cpp b/Framework/PythonInterface/mantid/geometry/src/Exports/Component.cpp
index 268245abcb4b8ceb7551ae353f9f25840beadb18..8ea305a1fbecb606b19841418b4092df23149e27 100644
--- a/Framework/PythonInterface/mantid/geometry/src/Exports/Component.cpp
+++ b/Framework/PythonInterface/mantid/geometry/src/Exports/Component.cpp
@@ -9,6 +9,7 @@ using namespace boost::python;
 namespace {
 #ifdef __clang__
 #pragma clang diagnostic push
+#pragma clang diagnostic ignored "-Wunknown-pragmas"
 #pragma clang diagnostic ignored "-Wunused-local-typedef"
 #endif
 // Default parameter function overloads
diff --git a/Framework/PythonInterface/mantid/geometry/src/Exports/Goniometer.cpp b/Framework/PythonInterface/mantid/geometry/src/Exports/Goniometer.cpp
index 71bf1e317994a90e509ac5dbbb3a7fa4411b24d0..50993f31ec81d475bb0c211231f29e84f68ca4c4 100644
--- a/Framework/PythonInterface/mantid/geometry/src/Exports/Goniometer.cpp
+++ b/Framework/PythonInterface/mantid/geometry/src/Exports/Goniometer.cpp
@@ -15,6 +15,7 @@ namespace //<unnamed>
 ///@cond
 #ifdef __clang__
 #pragma clang diagnostic push
+#pragma clang diagnostic ignored "-Wunknown-pragmas"
 #pragma clang diagnostic ignored "-Wunused-local-typedef"
 #endif
 // define overloaded functions
diff --git a/Framework/PythonInterface/mantid/kernel/src/Exports/ConfigService.cpp b/Framework/PythonInterface/mantid/kernel/src/Exports/ConfigService.cpp
index 2a29d8d14119e30fe3a12daceb180f3be76d832d..22a6c099010b426e969319b0d978d85180b45722 100644
--- a/Framework/PythonInterface/mantid/kernel/src/Exports/ConfigService.cpp
+++ b/Framework/PythonInterface/mantid/kernel/src/Exports/ConfigService.cpp
@@ -30,6 +30,7 @@ std::string getStringUsingCache(ConfigServiceImpl &self,
 
 #ifdef __clang__
 #pragma clang diagnostic push
+#pragma clang diagnostic ignored "-Wunknown-pragmas"
 #pragma clang diagnostic ignored "-Wunused-local-typedef"
 #endif
 
diff --git a/Framework/PythonInterface/mantid/kernel/src/Exports/Statistics.cpp b/Framework/PythonInterface/mantid/kernel/src/Exports/Statistics.cpp
index 086feee3bc4c0a1de33b2b36d9c30a78b6bee467..d2f9494ae0059a2f4839abd506fcf8da627f4c0c 100644
--- a/Framework/PythonInterface/mantid/kernel/src/Exports/Statistics.cpp
+++ b/Framework/PythonInterface/mantid/kernel/src/Exports/Statistics.cpp
@@ -96,6 +96,7 @@ Statistics getStatisticsNumpy(const numeric::array &data,
 
 #ifdef __clang__
 #pragma clang diagnostic push
+#pragma clang diagnostic ignored "-Wunknown-pragmas"
 #pragma clang diagnostic ignored "-Wunused-local-typedef"
 #endif
 // Define an overload to handle the default argument
@@ -154,6 +155,7 @@ std::vector<double> getModifiedZscoreNumpy(const numeric::array &data,
 
 #ifdef __clang__
 #pragma clang diagnostic push
+#pragma clang diagnostic ignored "-Wunknown-pragmas"
 #pragma clang diagnostic ignored "-Wunused-local-typedef"
 #endif
 // Define an overload to handle the default argument
@@ -214,6 +216,7 @@ std::vector<double> getMomentsAboutOriginNumpy(const numeric::array &indep,
 
 #ifdef __clang__
 #pragma clang diagnostic push
+#pragma clang diagnostic ignored "-Wunknown-pragmas"
 #pragma clang diagnostic ignored "-Wunused-local-typedef"
 #endif
 // Define an overload to handle the default argument
@@ -235,6 +238,7 @@ std::vector<double> getMomentsAboutMeanNumpy(const numeric::array &indep,
 
 #ifdef __clang__
 #pragma clang diagnostic push
+#pragma clang diagnostic ignored "-Wunknown-pragmas"
 #pragma clang diagnostic ignored "-Wunused-local-typedef"
 #endif
 // Define an overload to handle the default argument
diff --git a/Framework/PythonInterface/test/testhelpers/WorkspaceCreationHelperModule.cpp b/Framework/PythonInterface/test/testhelpers/WorkspaceCreationHelperModule.cpp
index 73cdc0f7d198a5366ef1d5fe27d10dafd9240fcc..9e6e57799eb3bf45edf789edfa54b8de0d873698 100644
--- a/Framework/PythonInterface/test/testhelpers/WorkspaceCreationHelperModule.cpp
+++ b/Framework/PythonInterface/test/testhelpers/WorkspaceCreationHelperModule.cpp
@@ -23,6 +23,7 @@ using namespace WorkspaceCreationHelper;
 
 #ifdef __clang__
 #pragma clang diagnostic push
+#pragma clang diagnostic ignored "-Wunknown-pragmas"
 #pragma clang diagnostic ignored "-Wunused-local-typedef"
 #endif
 BOOST_PYTHON_FUNCTION_OVERLOADS(create2DWorkspaceWithFullInstrument_overloads,