Currently the three faculties: Faculty of Engineering; Faculty of Computing and Faculty of Management and Social Sciences are functional at the CUST.
The Faculty of Engineering houses the departments of Electrical Engineering, Mechanical Engineering and Civil Engineering.
Faculty of Computing comprises of the Department of Computer Sciences, Department of Bioinformatics & Biosciences and Department of Mathematics.
Whereas the Faculty of Management and Social Sciences accommodates the departments of Management, Finance and Economics.
To guarantee the acceptability of the degrees offered by CUST nationally and internationally, the university offers a semester system and follows many international standards and norms of higher education. Many of the rules and policies of the university are in compliance to international standards of education. The Academic programs such as BS, MS and PhD all are recognized by respective accreditation bodies of Pakistan. CUST has introduced Doctoral Programs in the following fields:
Other than offering academic qualifications, CUST also offers training programs and diplomas. Several workshops and seminars are run time to time by the University.