The University is governed by the Board of Management, the highest statutory body. Its membership is as per UGC guidelines.

The Planning and Monitoring Board meets periodically to review the progress in implementing policies and developing strategic plans for the University.

The Finance Committee monitors the flow of funds and approves the university's budget. This committee also scrutinises the University's audited statement of accounts.

The Academic Council, the university's most significant statutory body, ensures high-quality educational programs. Its members come from renowned institutions and organisations and advise on framing regulations, curricula, and syllabi for the programs offered at JU. The Vice-Chancellor is the Chairman of this Council.

Each faculty has a Board of Studies whose members are domain experts from the industry and other renowned institutions and from within, giving directions for any changes required for the success of the academic programs.