diff --git a/examples/apps/cli/main.c b/examples/apps/cli/main.c
index d7fa4fdd2..775295a1a 100644
--- a/examples/apps/cli/main.c
+++ b/examples/apps/cli/main.c
@@ -26,9 +26,14 @@
  *  POSSIBILITY OF SUCH DAMAGE.
  */
 
+#ifdef OPENTHREAD_CONFIG_FILE
+#include OPENTHREAD_CONFIG_FILE
+#else
+#include <openthread-config.h>
+#endif
+
 #include <openthread-core-config.h>
 #include <openthread.h>
-#include <openthread-config.h>
 #include <openthread-diag.h>
 #include <cli/cli-uart.h>
 #include <platform/platform.h>
diff --git a/examples/apps/ncp/main.c b/examples/apps/ncp/main.c
index 7173d47bb..6764dbd08 100644
--- a/examples/apps/ncp/main.c
+++ b/examples/apps/ncp/main.c
@@ -26,9 +26,14 @@
  *  POSSIBILITY OF SUCH DAMAGE.
  */
 
+#ifdef OPENTHREAD_CONFIG_FILE
+#include OPENTHREAD_CONFIG_FILE
+#else
+#include <openthread-config.h>
+#endif
+
 #include <openthread-core-config.h>
 #include <openthread.h>
-#include <openthread-config.h>
 #include <openthread-diag.h>
 #include <common/debug.hpp>
 #include <ncp/ncp.h>
diff --git a/src/cli/cli.cpp b/src/cli/cli.cpp
index cae1043b7..9e47a9b48 100644
--- a/src/cli/cli.cpp
+++ b/src/cli/cli.cpp
@@ -31,12 +31,17 @@
  *   This file implements the CLI interpreter.
  */
 
+#ifdef OPENTHREAD_CONFIG_FILE
+#include OPENTHREAD_CONFIG_FILE
+#else
+#include <openthread-config.h>
+#endif
+
 #include <stdio.h>
 #include <stdlib.h>
 #include <string.h>
 
 #include <openthread.h>
-#include <openthread-config.h>
 #include <openthread-diag.h>
 #include <commissioning/commissioner.h>
 #include <commissioning/joiner.h>
diff --git a/src/cli/cli.hpp b/src/cli/cli.hpp
index 2630dfdcd..5df53bdd9 100644
--- a/src/cli/cli.hpp
+++ b/src/cli/cli.hpp
@@ -34,9 +34,13 @@
 #ifndef CLI_HPP_
 #define CLI_HPP_
 
-#include <stdarg.h>
-
+#ifdef OPENTHREAD_CONFIG_FILE
+#include OPENTHREAD_CONFIG_FILE
+#else
 #include <openthread-config.h>
+#endif
+
+#include <stdarg.h>
 
 #include <cli/cli_server.hpp>
 #include <net/icmp6.hpp>
diff --git a/src/cli/cli_dataset.cpp b/src/cli/cli_dataset.cpp
index 347acd767..7abbfc032 100644
--- a/src/cli/cli_dataset.cpp
+++ b/src/cli/cli_dataset.cpp
@@ -31,12 +31,17 @@
  *   This file implements the CLI interpreter.
  */
 
+#ifdef OPENTHREAD_CONFIG_FILE
+#include OPENTHREAD_CONFIG_FILE
+#else
+#include <openthread-config.h>
+#endif
+
 #include <stdio.h>
 #include <stdlib.h>
 #include <string.h>
 
 #include <openthread.h>
-#include <openthread-config.h>
 
 #include "cli.hpp"
 #include "cli_dataset.hpp"
diff --git a/src/core/crypto/mbedtls.hpp b/src/core/crypto/mbedtls.hpp
index 83e3349e4..2b349d43b 100644
--- a/src/core/crypto/mbedtls.hpp
+++ b/src/core/crypto/mbedtls.hpp
@@ -34,7 +34,12 @@
 #ifndef OT_MBEDTLS_HPP_
 #define OT_MBEDTLS_HPP_
 
+#ifdef OPENTHREAD_CONFIG_FILE
+#include OPENTHREAD_CONFIG_FILE
+#else
 #include <openthread-config.h>
+#endif
+
 #include <mbedtls/memory_buffer_alloc.h>
 
 namespace Thread {
diff --git a/src/core/mac/mac.cpp b/src/core/mac/mac.cpp
index f42b5a819..1bd158282 100644
--- a/src/core/mac/mac.cpp
+++ b/src/core/mac/mac.cpp
@@ -31,9 +31,13 @@
  *   This file implements the subset of IEEE 802.15.4 primitives required for Thread.
  */
 
-#include <string.h>
-
+#ifdef OPENTHREAD_CONFIG_FILE
+#include OPENTHREAD_CONFIG_FILE
+#else
 #include <openthread-config.h>
+#endif
+
+#include <string.h>
 
 #include <common/code_utils.hpp>
 #include <common/debug.hpp>
diff --git a/src/core/meshcop/commissioner.cpp b/src/core/meshcop/commissioner.cpp
index 33edd2fb7..7b03aef94 100644
--- a/src/core/meshcop/commissioner.cpp
+++ b/src/core/meshcop/commissioner.cpp
@@ -31,9 +31,13 @@
  *   This file implements a Commissioner role.
  */
 
-#include <stdio.h>
-
+#ifdef OPENTHREAD_CONFIG_FILE
+#include OPENTHREAD_CONFIG_FILE
+#else
 #include <openthread-config.h>
+#endif
+
+#include <stdio.h>
 
 #include <coap/coap_header.hpp>
 #include <common/logging.hpp>
diff --git a/src/core/meshcop/joiner.cpp b/src/core/meshcop/joiner.cpp
index a970784b3..bb45f2a68 100644
--- a/src/core/meshcop/joiner.cpp
+++ b/src/core/meshcop/joiner.cpp
@@ -31,11 +31,15 @@
  *   This file implements the Joiner role.
  */
 
+#ifdef OPENTHREAD_CONFIG_FILE
+#include OPENTHREAD_CONFIG_FILE
+#else
+#include <openthread-config.h>
+#endif
+
 #include <assert.h>
 #include <stdio.h>
 
-#include <openthread-config.h>
-
 #include <common/code_utils.hpp>
 #include <common/encoding.hpp>
 #include <common/logging.hpp>
diff --git a/src/core/openthread.cpp b/src/core/openthread.cpp
index 10a6424bb..089fab2f9 100644
--- a/src/core/openthread.cpp
+++ b/src/core/openthread.cpp
@@ -31,8 +31,13 @@
  *   This file implements the top-level interface to the OpenThread stack.
  */
 
-#include <openthread.h>
+#ifdef OPENTHREAD_CONFIG_FILE
+#include OPENTHREAD_CONFIG_FILE
+#else
 #include <openthread-config.h>
+#endif
+
+#include <openthread.h>
 #include <common/code_utils.hpp>
 #include <common/debug.hpp>
 #include <common/logging.hpp>
diff --git a/src/core/thread/thread_netif.hpp b/src/core/thread/thread_netif.hpp
index 1734113ad..3ab341805 100644
--- a/src/core/thread/thread_netif.hpp
+++ b/src/core/thread/thread_netif.hpp
@@ -34,7 +34,12 @@
 #ifndef THREAD_NETIF_HPP_
 #define THREAD_NETIF_HPP_
 
+#ifdef OPENTHREAD_CONFIG_FILE
+#include OPENTHREAD_CONFIG_FILE
+#else
 #include <openthread-config.h>
+#endif
+
 #include <openthread-types.h>
 
 #include <mac/mac.hpp>
diff --git a/src/ncp/ncp_base.hpp b/src/ncp/ncp_base.hpp
index 27d711ebe..71b462eb1 100644
--- a/src/ncp/ncp_base.hpp
+++ b/src/ncp/ncp_base.hpp
@@ -33,8 +33,13 @@
 #ifndef NCP_BASE_HPP_
 #define NCP_BASE_HPP_
 
-#include <openthread-types.h>
+#ifdef OPENTHREAD_CONFIG_FILE
+#include OPENTHREAD_CONFIG_FILE
+#else
 #include <openthread-config.h>
+#endif
+
+#include <openthread-types.h>
 #include <common/message.hpp>
 #include <common/tasklet.hpp>