Delete users in Project Server 2013

To delete resources and users

1. On the Project Web App home page, on the Settings menu, click PWA Settings.
2. On the Server Settings page, in the Queue and Database Administration section, click Delete Enterprise Objects.
3. On the Delete Enterprise Objects page, select the Resources and Users option.
4. Select the user or resource that you want to delete.
5. Click Delete.
6. On the confirmation dialog box, click OK.

https://technet.microsoft.com/en-us/library/gg702622.aspx