diff --git a/tools/Config.mk b/tools/Config.mk
index 2b43c26eb2..eea069a71c 100644
--- a/tools/Config.mk
+++ b/tools/Config.mk
@@ -138,10 +138,11 @@ endif
 # Process board-specific directories
 
 ifeq ($(CONFIG_ARCH_BOARD_CUSTOM),y)
+	CUSTOM_DIR = $(patsubst "%",%,$(CONFIG_ARCH_BOARD_CUSTOM_DIR))
 ifeq ($(CONFIG_ARCH_BOARD_CUSTOM_DIR_RELPATH),y)
-  BOARD_DIR ?= $(TOPDIR)$(DELIM)$(CONFIG_ARCH_BOARD_CUSTOM_DIR)
+  BOARD_DIR ?= $(TOPDIR)$(DELIM)$(CUSTOM_DIR)
 else
-  BOARD_DIR ?= $(CONFIG_ARCH_BOARD_CUSTOM_DIR)
+  BOARD_DIR ?= $(CUSTOM_DIR)
 endif
 else
   BOARD_DIR ?= $(TOPDIR)$(DELIM)boards$(DELIM)$(CONFIG_ARCH)$(DELIM)$(CONFIG_ARCH_CHIP)$(DELIM)$(CONFIG_ARCH_BOARD)