Yes, you can

The eligibility criteria for JEE Mains as set by the NTA is as follows:

• There is no age limit and you need to pass12th Board Examination or any equivalent qualifying examination with Physics, Mathematics as compulsory subjects along with Chemistry, Biotechnology, Biology and technical vocational as one of the subjects.

As you do  fit the criteria, you can write jee after bsc computer science and can  get admission in NIT's for mcs or mtech.