yes that is possible.
You need a GitHub object and get your repository via that.
GitHub github = GitHub.connectToEnterpriseWithOAuth(API_URL,
USER,
TOKEN);
GHRepository ghRepo = github.getRepository(Name of your Repo);
GHPullRequest newPr = ghRepo.createPullRequest(String title, String head, String base, String body);
The newPr is created at the specified repository. You can use the Object newPr to set more data in your pull request.