Professor Dr. Golam Mowlah is the founder vice-chancellor of Comilla University who served the until he was removed on July 30 2008 and Zulfikar Ali, a professor of mathematics, was given the charge. The next vice-chancellor of Comilla University, Dr. A.K.M. Zehadul Karim declared his resignation on 7 October 2009 after violence. Professor Amir Hossen Khan, a professor of Physics department of Jahangirnagar University, was appointed as VC on 22 November 2009. The chancellor of the university is Honorable President of Bangladesh Zillur Rahman.
It started with seven departments. Now there are a total of fourteen department including Computer Science & Engineering (CSE), Information & Communication Technology (ICT), Physics, Chemistry, Statistics, Mathematics, Accounting & Information Systems (AIS), Marketing, Management Studies, Economics, Public Administration, Anthropology, Bengali, and English. Three more departments were announced to be opened from 2012. The residence hall facilities are available, namely- Shahid Dhirendranath Dutta Hall, Kazi Nazrul Islam Hall, and Nawab Faizunnesa Chowdhurani Hall.