Indian Maritime University offers two M.B.A. Programmes; M.B.A. in Port and Shipping Management and M.B.A. in International Transportation and Logistics Management. The duration of the MBA programme is two academic years consisting of four semesters. Each academic year shall be divided into two semesters. The odd semester is scheduled from August to January of each academic year and the even semesters from February to July of each academic year. There shall be not less than 90 working days for each semester.

M.B.A. in Port and Shipping Management is designed to provide the students with adequate skills and knowledge in functional areas of the port and shipping sectors. It also gives a holistic view of the sector integrating various areas viz. port management, maritime law and maritime economics which helps them to gain a thorough understanding of the maritime business and taking up employment in the same.

M.B.A. in International Transportation and Logistics Management is a program designed to provide an exposure to 'Management of the domestic and international modes of Transportation' in today’s rapidly changing economic scenario. Logistics management assumes a systematic approach to deal with a wide variety of activities related to movement of traffic from origin to destination point.