diff --git a/src/holoscan_cli/container/core.py b/src/holoscan_cli/container/core.py
index 1bdc9c6..f3cb62c 100644
--- a/src/holoscan_cli/container/core.py
+++ b/src/holoscan_cli/container/core.py
@@ -549,7 +549,12 @@ def run(
     ) -> None:
         """Launch the container"""
 
-        if not self.dryrun:
+        default_run_args = shlex.split(HoloscanContainer.DEFAULT_DOCKER_RUN_ARGS or "")
+        extra_run_args = shlex.split(docker_opts or "")
+        configured_runtime = get_cli_arg_value(default_run_args + extra_run_args, "--runtime")
+        runtime = configured_runtime or "nvidia"
+
+        if not self.dryrun and runtime == "nvidia":
             check_nvidia_ctk()
 
         if local_sdk_root is not None:
@@ -562,8 +567,6 @@ def run(
         # If the caller already supplies --cidfile (via DEFAULT_DOCKER_RUN_ARGS or
         # docker_opts), use that path for cleanup and skip injecting our own —
         # Docker rejects duplicate --cidfile flags.
-        default_run_args = shlex.split(HoloscanContainer.DEFAULT_DOCKER_RUN_ARGS or "")
-        extra_run_args = shlex.split(docker_opts or "")
         explicit_cidfile = get_cli_arg_value(default_run_args + extra_run_args, "--cidfile")
         internal_cidfile: Optional[Path] = None
         if explicit_cidfile:
@@ -579,7 +582,7 @@ def run(
             cmd.extend(["--cidfile", str(internal_cidfile)])
         cmd.extend(self.get_security_args(as_root))
         cmd.extend(self.get_volume_args(add_volumes, enable_mps))
-        cmd.extend(self.get_gpu_runtime_args())
+        cmd.extend(self.get_gpu_runtime_args(None if configured_runtime is not None else runtime))
         cmd.extend(self.get_environment_args())
 
         cmd.extend(self.get_conditional_options(use_tini, persistent))
@@ -733,9 +736,12 @@ def get_device_cgroup_args(self) -> List[str]:
             "c 189:* rmw",  # /dev/bus/usb/*
         ]
 
-    def get_gpu_runtime_args(self) -> List[str]:
+    def get_gpu_runtime_args(self, runtime: Optional[str] = "nvidia") -> List[str]:
         args = []
-        args.extend(self.get_nvidia_runtime_args())
+        if runtime == "nvidia":
+            args.extend(self.get_nvidia_runtime_args())
+        elif runtime is not None:
+            args.extend(["--runtime", runtime])
         args.extend(
             [
                 "--cap-add",
diff --git a/tests/unit/test_container_core.py b/tests/unit/test_container_core.py
index 1d49b8c..ea4688c 100644
--- a/tests/unit/test_container_core.py
+++ b/tests/unit/test_container_core.py
@@ -493,15 +493,15 @@ def test_build_dryrun_omits_base_sdk_version_when_not_configured(tmp_path, monke
     assert not any(arg.startswith("BASE_SDK_VERSION=") for arg in first)
 
 
-def test_run_dryrun_assembles_docker_command_without_runtime_checks(tmp_path, monkeypatch):
-    """Dry-run container launch covers docker-run argument composition while
-    skipping NVIDIA runtime validation and the real docker command."""
+def test_run_assembles_docker_command_without_ctk_for_custom_runtime(tmp_path, monkeypatch):
+    """A custom Docker runtime bypasses NVIDIA Container Toolkit validation."""
     project_dir = tmp_path / "applications" / "my_app"
     project_dir.mkdir(parents=True)
     (project_dir / "Dockerfile").write_text("FROM scratch\n", encoding="utf-8")
     volume = tmp_path / "input-data"
     volume.mkdir()
     calls = []
+    ctk_checks = []
     monkeypatch.delenv("DISPLAY", raising=False)
     monkeypatch.delenv("WAYLAND_DISPLAY", raising=False)
     monkeypatch.delenv("HOLOSCAN_CLI_ENABLE_SCCACHE", raising=False)
@@ -510,6 +510,7 @@ def test_run_dryrun_assembles_docker_command_without_runtime_checks(tmp_path, mo
     monkeypatch.setattr(container_core, "get_image_pythonpath", lambda img, dryrun: "/image/python")
     monkeypatch.setattr(container_core, "get_group_id", lambda group: {"video": 44}.get(group))
     monkeypatch.setattr(container_core, "run_command", lambda cmd, **kwargs: calls.append(cmd))
+    monkeypatch.setattr(container_core, "check_nvidia_ctk", lambda: ctk_checks.append(True))
 
     c = _stub_container(
         tmp_path,
@@ -519,7 +520,6 @@ def test_run_dryrun_assembles_docker_command_without_runtime_checks(tmp_path, mo
             "metadata": {"language": "python"},
         },
     )
-    c.dryrun = True
     c.verbose = True
 
     c.run(
@@ -527,7 +527,7 @@ def test_run_dryrun_assembles_docker_command_without_runtime_checks(tmp_path, mo
         use_tini=True,
         persistent=False,
         as_root=False,
-        docker_opts="--name smoke --cidfile /tmp/custom.cid",
+        docker_opts="--name smoke --cidfile /tmp/custom.cid --runtime runc",
         add_volumes=[str(volume)],
         nsys_profile=True,
         nsys_location="/opt/nsys",
@@ -555,6 +555,8 @@ def test_run_dryrun_assembles_docker_command_without_runtime_checks(tmp_path, mo
     assert "NGC_CLI_ORG=nvidia" in cmd
     assert "--name" in cmd
     assert "/tmp/custom.cid" in cmd
+    assert container_core.get_cli_arg_value(cmd, "--runtime") == "runc"
+    assert not ctk_checks
     assert cmd[-4:] == ["custom:image", "bash", "-lc", "echo ok"]