diff --git a/Source/Core/VideoCommon/ShaderGenCommon.cpp b/Source/Core/VideoCommon/ShaderGenCommon.cpp
index 53cf3edf61..c5cd3ef30d 100644
--- a/Source/Core/VideoCommon/ShaderGenCommon.cpp
+++ b/Source/Core/VideoCommon/ShaderGenCommon.cpp
@@ -87,6 +87,24 @@ std::string GetDiskShaderCacheFileName(APIType api_type, const char* type, bool
   return filename;
 }
 
+void WriteIsNanHeader(ShaderCode& out, APIType api_type)
+{
+  if (api_type == APIType::D3D)
+  {
+    out.Write("bool dolphin_isnan(float f) {{\n"
+              "  // Workaround for the HLSL compiler deciding that isnan can never be true and\n"
+              "  // optimising away the call, even though the value can actually be NaN\n"
+              "  // Just look for the bit pattern that indicates NaN instead\n"
+              "  return (asint(f) & 0x7FFFFFFF) > 0x7F800000;\n"
+              "}}\n\n");
+    // If isfinite is needed, (asint(f) & 0x7F800000) != 0x7F800000 can be used
+  }
+  else
+  {
+    out.Write("#define dolphin_isnan(f) isnan(f)\n");
+  }
+}
+
 static void DefineOutputMember(ShaderCode& object, APIType api_type, std::string_view qualifier,
                                std::string_view type, std::string_view name, int var_index,
                                std::string_view semantic = {}, int semantic_index = -1)
diff --git a/Source/Core/VideoCommon/ShaderGenCommon.h b/Source/Core/VideoCommon/ShaderGenCommon.h
index 2a1dcf1215..3c1e7f38f8 100644
--- a/Source/Core/VideoCommon/ShaderGenCommon.h
+++ b/Source/Core/VideoCommon/ShaderGenCommon.h
@@ -176,6 +176,8 @@ union ShaderHostConfig
 std::string GetDiskShaderCacheFileName(APIType api_type, const char* type, bool include_gameid,
                                        bool include_host_config, bool include_api = true);
 
+void WriteIsNanHeader(ShaderCode& out, APIType api_type);
+
 void GenerateVSOutputMembers(ShaderCode& object, APIType api_type, u32 texgens,
                              const ShaderHostConfig& host_config, std::string_view qualifier);
 
diff --git a/Source/Core/VideoCommon/UberShaderVertex.cpp b/Source/Core/VideoCommon/UberShaderVertex.cpp
index 5b02b1f989..70b434b786 100644
--- a/Source/Core/VideoCommon/UberShaderVertex.cpp
+++ b/Source/Core/VideoCommon/UberShaderVertex.cpp
@@ -50,6 +50,7 @@ ShaderCode GenVertexShader(APIType api_type, const ShaderHostConfig& host_config
   out.Write("}};\n\n");
 
   WriteUberShaderCommonHeader(out, api_type, host_config);
+  WriteIsNanHeader(out, api_type);
   WriteLightingFunction(out);
 
   if (api_type == APIType::OpenGL || api_type == APIType::Vulkan)
@@ -438,9 +439,9 @@ static void GenVertexShaderTexGens(APIType api_type, u32 num_texgen, ShaderCode&
   // Convert NaNs to 1 - needed to fix eyelids in Shadow the Hedgehog during cutscenes
   // See https://bugs.dolphin-emu.org/issues/11458
   out.Write("  // Convert NaN to 1\n");
-  out.Write("  if (isnan(coord.x)) coord.x = 1.0;\n");
-  out.Write("  if (isnan(coord.y)) coord.y = 1.0;\n");
-  out.Write("  if (isnan(coord.z)) coord.z = 1.0;\n");
+  out.Write("  if (dolphin_isnan(coord.x)) coord.x = 1.0;\n");
+  out.Write("  if (dolphin_isnan(coord.y)) coord.y = 1.0;\n");
+  out.Write("  if (dolphin_isnan(coord.z)) coord.z = 1.0;\n");
 
   out.Write("  // first transformation\n");
   out.Write("  uint texgentype = {};\n", BitfieldExtract<&TexMtxInfo::texgentype>("texMtxInfo"));
diff --git a/Source/Core/VideoCommon/VertexShaderGen.cpp b/Source/Core/VideoCommon/VertexShaderGen.cpp
index 4e4121b564..25fb5a06c5 100644
--- a/Source/Core/VideoCommon/VertexShaderGen.cpp
+++ b/Source/Core/VideoCommon/VertexShaderGen.cpp
@@ -96,7 +96,9 @@ ShaderCode GenerateVertexShaderCode(APIType api_type, const ShaderHostConfig& ho
 
   out.Write("struct VS_OUTPUT {{\n");
   GenerateVSOutputMembers(out, api_type, uid_data->numTexGens, host_config, "");
-  out.Write("}};\n");
+  out.Write("}};\n\n");
+
+  WriteIsNanHeader(out, api_type);
 
   if (api_type == APIType::OpenGL || api_type == APIType::Vulkan)
   {
@@ -335,9 +337,9 @@ ShaderCode GenerateVertexShaderCode(APIType api_type, const ShaderHostConfig& ho
     // Convert NaNs to 1 - needed to fix eyelids in Shadow the Hedgehog during cutscenes
     // See https://bugs.dolphin-emu.org/issues/11458
     out.Write("// Convert NaN to 1\n");
-    out.Write("if (isnan(coord.x)) coord.x = 1.0;\n");
-    out.Write("if (isnan(coord.y)) coord.y = 1.0;\n");
-    out.Write("if (isnan(coord.z)) coord.z = 1.0;\n");
+    out.Write("if (dolphin_isnan(coord.x)) coord.x = 1.0;\n");
+    out.Write("if (dolphin_isnan(coord.y)) coord.y = 1.0;\n");
+    out.Write("if (dolphin_isnan(coord.z)) coord.z = 1.0;\n");
 
     // first transformation
     switch (texinfo.texgentype)