The Master of Science in Mathematics program consists of course work plus a Major Research Paper (MRP) or Thesis. The Thesis route is available as a two-year (6 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.​​​​​​

The thesis route requires students to become more deeply proficient in an area of mathematics than is standard in an MRP. A thesis is generally (depending on the topic) longer and more detailed than an MRP. Because of its more advanced nature, a thesis requires more time to complete than an MRP. Additionally, a thesis generally (but not always) contains multi- and inter-disciplinary aspects, and will usually involve research into advanced areas of mathematics and computational science.