The Master of Computer Applications (MCA) program at NIT Calicut (the Institute's name was then "Regional Engineering College (REC) Calicut”) commenced in the year 1988 under the Department of Electrical & Electronics Engineering (EEE). Later, in 1997, the Department of Computer Science & Engineering (CSED) became an independent department, and the MCA program continued under CSED. The MCA program was a full-time postgraduate course designed to equip students with both theoretical knowledge and practical expertise in the core areas of computer science. With a program duration of three years (six semesters), the program emphasized strong foundations in software engineering, algorithms, data structures, databases, and system-level design, while also offering electives in cutting-edge domains such as Artificial Intelligence, cybersecurity, cloud computing, and mobile app development. The admission was offered through the prestigious NIMCET examination, attracting some of the brightest minds from across the country, with an annual intake of 50 students. 

Students benefited from a rigorous curriculum supported by experienced faculty from the Department of Computer Science and Engineering and the Mathematics Department of REC/NIT Calicut. The final semester was devoted to a capstone project that encouraged innovation and real-world problem-solving. Graduates of the program went on to successful careers in top-tier companies such as Oracle, CISCO, Deloitte, etc. NIT Calicut's MCA alumni also serve as faculty in top-tier universities such as Chennai Mathematical Institute and the University of Leeds.

While the MCA program was formally phased out in 2022 as part of academic restructuring, it remains an integral chapter in the institute’s academic history. The contributions of its alumni continue to be reflected in academia, industry, and entrepreneurial ventures both in India and abroad.