diff --git a/.github/workflows/otbr.yml b/.github/workflows/otbr.yml
index 368dc72df..6f9412b86 100644
--- a/.github/workflows/otbr.yml
+++ b/.github/workflows/otbr.yml
@@ -113,31 +113,43 @@ jobs:
             otbr_trel: 0
             cert_scripts: ./tests/scripts/thread-cert/border_router/*.py
             packet_verification: 1
+            nat64: 0
             description: ""
           - otbr_mdns: "mDNSResponder"
             otbr_trel: 1
             cert_scripts: ./tests/scripts/thread-cert/border_router/*.py
             packet_verification: 2
+            nat64: 0
             description: ""
           - otbr_mdns: "mDNSResponder"
             otbr_trel: 0
             cert_scripts: ./tests/scripts/thread-cert/border_router/MATN/*.py
             packet_verification: 1
+            nat64: 0
             description: "MATN"
           - otbr_mdns: "mDNSResponder"
             otbr_trel: 0
             cert_scripts: ./tests/scripts/thread-cert/border_router/LowPower/*.py
             packet_verification: 1
+            nat64: 0
             description: "LowPower"
+          - otbr_mdns: "mDNSResponder"
+            otbr_trel: 0
+            cert_scripts: ./tests/scripts/thread-cert/border_router/nat64/*.py
+            packet_verification: 1
+            nat64: 1
+            description: "nat64"
           - otbr_mdns: "avahi"
             otbr_trel: 0
             cert_scripts: ./tests/scripts/thread-cert/border_router/*.py
             packet_verification: 1
+            nat64: 0
             description: ""
           - otbr_mdns: "avahi"
             otbr_trel: 1
             cert_scripts: ./tests/scripts/thread-cert/border_router/*.py
             packet_verification: 2
+            nat64: 0
             description: ""
     name: BR ${{ matrix.description }} (${{ matrix.otbr_mdns }}, TREL=${{matrix.otbr_trel}})
     env:
@@ -152,6 +164,7 @@ jobs:
       PYTHONUNBUFFERED: 1
       VERBOSE: 1
       BORDER_ROUTING: 1
+      NAT64: ${{ matrix.nat64 }}
       MAX_JOBS: 3
     steps:
     - uses: actions/checkout@v2
diff --git a/script/test b/script/test
index 631013ad2..411c88664 100755
--- a/script/test
+++ b/script/test
@@ -324,7 +324,7 @@ do_build_otbr_docker()
             --build-arg BACKBONE_ROUTER=1 \
             --build-arg REFERENCE_DEVICE=1 \
             --build-arg OT_BACKBONE_CI=1 \
-            --build-arg NAT64=0 \
+            --build-arg NAT64="${NAT64:-0}" \
             --build-arg REST_API=0 \
             --build-arg WEB_GUI=0 \
             --build-arg MDNS="${OTBR_MDNS:-mDNSResponder}" \
diff --git a/tests/scripts/thread-cert/border_router/test_nat64_multi_border_routers.py b/tests/scripts/thread-cert/border_router/nat64/test_multi_border_routers.py
similarity index 100%
rename from tests/scripts/thread-cert/border_router/test_nat64_multi_border_routers.py
rename to tests/scripts/thread-cert/border_router/nat64/test_multi_border_routers.py
diff --git a/tests/scripts/thread-cert/border_router/test_nat64_single_border_router.py b/tests/scripts/thread-cert/border_router/nat64/test_single_border_router.py
similarity index 100%
rename from tests/scripts/thread-cert/border_router/test_nat64_single_border_router.py
rename to tests/scripts/thread-cert/border_router/nat64/test_single_border_router.py