diff --git a/boards/rt1060/CMakeLists.txt b/boards/rt1060/CMakeLists.txt
index 955d2a0d..c420e4e6 100644
--- a/boards/rt1060/CMakeLists.txt
+++ b/boards/rt1060/CMakeLists.txt
@@ -44,8 +44,15 @@ else()
     list(APPEND BOARD_SOURCES evkbimxrt1060/pin_mux.c)
     list(APPEND BOARD_SOURCES evkbimxrt1060/clock_config.c)
     list(APPEND BOARD_INCLUDE_DIRECTORIES evkbimxrt1060)
-    set(BOARD_1ST_UART_INSTANCE 1)
-    set(BOARD_2ND_UART_INSTANCE 2)
+endif()
+
+if("${EVK_RT1060_BOARD}" STREQUAL "evkbmimxrt1060")
+    if (NOT DEFINED BOARD_1ST_UART_INSTANCE)
+        set(BOARD_1ST_UART_INSTANCE 1)
+    endif()
+    if (NOT DEFINED BOARD_2ND_UART_INSTANCE)
+        set(BOARD_2ND_UART_INSTANCE 2)
+    endif()
 endif()
 
 list(APPEND BOARD_COMPILE_DEFINITIONS_PUBLIC)
diff --git a/boards/rt1060/evkbimxrt1060/pin_mux.c b/boards/rt1060/evkbimxrt1060/pin_mux.c
index 7c41b5f1..dea63967 100644
--- a/boards/rt1060/evkbimxrt1060/pin_mux.c
+++ b/boards/rt1060/evkbimxrt1060/pin_mux.c
@@ -37,7 +37,9 @@ void BOARD_InitBootPins(void)
 {
     BOARD_InitPins();
     BOARD_InitDEBUG_UARTPins();
+#if !defined(CONFIG_NCP) || defined(CONFIG_NCP_UART)
     BOARD_InitArduinoUARTPins();
+#endif
 #if defined(SDIO_ENABLED)
     BOARD_InitUSDHCPins();
 #endif
diff --git a/script/build_rt1060 b/script/build_rt1060
index 8f871b45..fb401d3c 100755
--- a/script/build_rt1060
+++ b/script/build_rt1060
@@ -114,7 +114,8 @@ readonly OT_OPTIONS_TRANSCEIVER_RW612=(
     "-DOT_NXP_TRANSCEIVER=rw612"
     "-DOT_NCP_RTOS_HOST=ON"
     "-DOT_NXP_LWIP=OFF"
-    "-DBOARD_APP_UART_INSTANCE=2"
+    "-DBOARD_1ST_UART_INSTANCE=2"
+    "-DBOARD_2ND_UART_INSTANCE=1"
     "-DEVK_RT1060_BOARD=evkbmimxrt1060"
     "-DFREERTOS_CONFIG_FILE_DIRECTORY=${OT_SRCDIR}/boards/rt1060/freertos/ncp_host"
 )