The Master of Science in Mathematics program consists of course work plus a Major Research Paper (MRP) or Thesis. The MRP route is a one-year (3 term) full-time program. Nipissing University's program trains students for future work in research, industry, business, or government, and provides a strong background in foundational areas of mathematics. The faculty members are experts in topology, analysis, combinatorics and graph theory, industrial and applied mathematics, with research in scheduling, computational problems, numerical mathematics, and optimization. Many faculty work on inter- and multi-disciplinary research in geography, the physical and health sciences, business, and management, to name only a few. Graduate students therefore also have an opportunity to perform research on the interface of mathematics and other disciplines.​​​​​​

Through the MRP, the student must show the ability to work independently in a scholarly manner. The MRP does not have to make a significant original contribution to academic knowledge of the subject, but it must display extensive research and independent analysis. Students must demonstrate a comprehensive knowledge and understanding of the literature relating to the topic.