NJIT offers an extremely flexible Masters program that encourages students to contribute to an individualized plan of study that builds upon the strengths of their B.S. and develop expertise in an area of concentration leading to careers in research and/or product development, or to prepare for further study in medicine, dentistry, law, and management, or for a Ph.D. in biomedical engineering. Major areas in which NJIT offers courses and conducts research are bioinstrumentation, biomaterials and tissue engineering, biomechanics, neural engineering and rehabilitation engineering.

Over the past several years, the M.S. in Biomedical Engineering program at NJIT currently has graduated the largest number of M.S. degrees in BME in the nation. The department offers a comprehensive set of courses specifically in biomedical engineering (usually 14-16 per semester), which are augmented by related engineering and life science courses taught in other departments.

 NJIT's location, in the middle of the nation's largest concentration of biomedical industries, provides access to expert instructors who offer specialized courses, which add to the richness of the academic environment. These industries also support graduate internships and thesis work, and often provide employment after graduation. The NJIT campus is within walking distance of both the University of Medicine and Dentistry of New Jersey flagship campus and Rutgers University-Newark. 

Graduate education at the three institutions is enhanced by collaboration agreements that allow cross-registration for courses, use of libraries, and opportunities for independent research. This benefits biomedical engineering by opening the possibilities for M.S. students to take advanced biological and medical science courses in addition to engineering courses.