System.register([], function () {});

System.register("foo", [], function () {});

$ npm install babel-plugin-transform-system-register

{
  "plugins": [
    ["transform-system-register", {
      "moduleName": "foo",
      "systemGlobal": "SystemJS"
    }]
  ]
}

$ babel --plugins transform-system-register script.js

require("babel-core").transform("code", {
  plugins: [
    ["transform-system-register", {
      moduleName: "foo",
      systemGlobal: "SystemJS",
      map: function(name) {
        return normalize(name);
      }
    }]
  ]
});