The institute offers engineering degrees in branches such as computer science and engineering, information technology, electronics and communication, electrical and electronics, mechanical and civil engineering, along with postgraduate and doctoral programmes, and admits students to each through the university's central admission cell. What a candidate faces is therefore an application and selection process rather than an institute-specific written examination: registration on the university portal, submission of academic records, consideration of the national entrance test score where that is required, allotment of a branch by merit, and confirmation on payment of fees and verification of original documents. Seats are also offered under the state quota for Sikkim candidates and under other categories the university notifies. The branches on offer, the accepted entrance test, the intake and the fee structure appear in the admission notification.

Applicants to the engineering programmes must have passed, or be appearing in, the class 12 or equivalent examination from a recognised board with physics and mathematics as compulsory subjects together with one of chemistry, biology, biotechnology, computer science or another subject the university accepts. The minimum aggregate marks required in those subjects, whether a national entrance test score is compulsory for the year, and the relaxation available to reserved and state-quota candidates, are stated in the Sikkim Manipal University admission notification and must be verified there. Lateral entry into the second year is offered separately to diploma holders on the conditions given in the same document.