diff --git a/Makefile b/Makefile
index 5e7c1d854441..ee5896261d2f 100644
--- a/Makefile
+++ b/Makefile
@@ -981,7 +981,7 @@ KBUILD_CFLAGS += -falign-functions=64
 endif
 
 # arch Makefile may override CC so keep this after arch Makefile is included
-NOSTDINC_FLAGS += -nostdinc -isystem $(shell $(CC) -print-file-name=include)
+NOSTDINC_FLAGS += -nostdinc
 
 # warn about C99 declaration after statement
 KBUILD_CFLAGS += -Wdeclaration-after-statement
diff --git a/arch/arm64/lib/Makefile b/arch/arm64/lib/Makefile
index 0941180a86d3..29490be2546b 100644
--- a/arch/arm64/lib/Makefile
+++ b/arch/arm64/lib/Makefile
@@ -9,6 +9,8 @@ ifeq ($(CONFIG_KERNEL_MODE_NEON), y)
 obj-$(CONFIG_XOR_BLOCKS)	+= xor-neon.o
 CFLAGS_REMOVE_xor-neon.o	+= -mgeneral-regs-only
 CFLAGS_xor-neon.o		+= -ffreestanding
+# Enable <arm_neon.h>
+CFLAGS_xor-neon.o		+= -isystem $(shell $(CC) -print-file-name=include)
 endif
 
 lib-$(CONFIG_ARCH_HAS_UACCESS_FLUSHCACHE) += uaccess_flushcache.o
diff --git a/arch/nds32/Makefile b/arch/nds32/Makefile
index ccdca7142020..c17fc3a755c3 100644
--- a/arch/nds32/Makefile
+++ b/arch/nds32/Makefile
@@ -9,6 +9,8 @@ endif
 # Avoid generating FPU instructions
 arch-y  += -mno-ext-fpu-sp -mno-ext-fpu-dp -mfloat-abi=soft
 
+# Enable <nds32_intrinsic.h>
+KBUILD_CFLAGS	+= -isystem $(shell $(CC) -print-file-name=include)
 KBUILD_CFLAGS	+= $(call cc-option, -mno-sched-prolog-epilog)
 KBUILD_CFLAGS	+= -mcmodel=large
 
diff --git a/arch/powerpc/lib/Makefile b/arch/powerpc/lib/Makefile
index 99a7c9132422..9e5d0f413b71 100644
--- a/arch/powerpc/lib/Makefile
+++ b/arch/powerpc/lib/Makefile
@@ -65,5 +65,7 @@ obj-$(CONFIG_FTR_FIXUP_SELFTEST) += feature-fixups-test.o
 
 obj-$(CONFIG_ALTIVEC)	+= xor_vmx.o xor_vmx_glue.o
 CFLAGS_xor_vmx.o += -maltivec $(call cc-option,-mabi=altivec)
+# Enable <altivec.h>
+CFLAGS_xor_vmx.o += -isystem $(shell $(CC) -print-file-name=include)
 
 obj-$(CONFIG_PPC64) += $(obj64-y)
diff --git a/crypto/Makefile b/crypto/Makefile
index c633f15a0481..429c4d57458c 100644
--- a/crypto/Makefile
+++ b/crypto/Makefile
@@ -119,6 +119,8 @@ CFLAGS_aegis128-neon-inner.o += $(aegis128-cflags-y)
 CFLAGS_REMOVE_aegis128-neon-inner.o += -mgeneral-regs-only
 aegis128-$(CONFIG_CRYPTO_AEGIS128_SIMD) += aegis128-neon.o aegis128-neon-inner.o
 endif
+# Enable <arm_neon.h>
+CFLAGS_aegis128-neon-inner.o += -isystem $(shell $(CC) -print-file-name=include)
 
 obj-$(CONFIG_CRYPTO_PCRYPT) += pcrypt.o
 obj-$(CONFIG_CRYPTO_CRYPTD) += cryptd.o
diff --git a/lib/raid6/Makefile b/lib/raid6/Makefile
index c770570bfe4f..45e17619422b 100644
--- a/lib/raid6/Makefile
+++ b/lib/raid6/Makefile
@@ -14,6 +14,8 @@ hostprogs	+= mktables
 
 ifeq ($(CONFIG_ALTIVEC),y)
 altivec_flags := -maltivec $(call cc-option,-mabi=altivec)
+# Enable <altivec.h>
+altivec_flags += -isystem $(shell $(CC) -print-file-name=include)
 
 ifdef CONFIG_CC_IS_CLANG
 # clang ppc port does not yet support -maltivec when -msoft-float is
@@ -34,6 +36,8 @@ endif
 # ARM/NEON intrinsics in a non C99-compliant environment (such as the kernel)
 ifeq ($(CONFIG_KERNEL_MODE_NEON),y)
 NEON_FLAGS := -ffreestanding
+# Enable <arm_neon.h>
+NEON_FLAGS += -isystem $(shell $(CC) -print-file-name=include)
 ifeq ($(ARCH),arm)
 NEON_FLAGS += -march=armv7-a -mfloat-abi=softfp -mfpu=neon
 endif