If a repo belongs to an organization instead of a user, the request for the pulls does not work. I am on an enterprise version, as well.
For example:
https://github.company.com/api/v3/repos/<username>/<reponame>/pulls?head=<username>%3A<branchname>
I can make this work from curl by substituting the organization name for the username:
https://github.company.com/api/v3/repos/<orgname>/<reponame>/pulls?head=<orgname>%3A<branchname>