It is not actually clear when the Christian Union began but evidence points to the aftermath of the East African revival that took place in the 50's and 60's. By then the CU had a chairman and a committee working with him. There was also a patron. Over the years the leadership changed and the numbers increased and a CU constitution was developed in order to orderly guide activities and to stress the objectives of the union.
The CU currently operates under FOCUS-Uganda. It is interdenominational but has a doctrinal basis of faith for which each member must abide by. The doctrinal basis of faith is made up of fundamental truths of Christianity.
Considering this fact, the CU has only been working with churches that ascribe to that doctrinal basis of faith. This working relationship has seen many pastors being invited to speak to the CU members in the fellowships. Also, members have been advised to find local churches where they can exercise their spiritual gifting even when they have left the university. This relationship has furthered the growth of unity in the body of Christ, putting aside denominational differences.