The Department of Computer Science & Information Technology of Cotton University is located beside Dr. Surya Kumar Bhuyan Library and the Alumni House. It started as a computer centre under the erstwhile Cotton College on the 30th of July 2003, with funding from The North Eastern Council, Shillong. In the year 2004, this Centre was upgraded to a full-fledged department. In 2006, B.Sc. (Major) course in Computer Science was introduced. In the year 2007 the department also introduced the BCA course. Currently, the department offers B.Sc. and BCA at the UG level, and MCA at the PG level. It also offers Ph.D. course in Computer Science & IT.