NISER offers a 5-year integrated M.Sc. Programme in basic sciences after 10+2 years of schooling (or equivalent). At present the institute has four major schools, namely Biology, Chemistry, Mathematics and Physics. After successful completion of the academic requirements students are awarded a Master of Science degree in one of the four subjects: biology, chemistry, mathematics or physics. The programme has a balanced semester-based course structure with a flexible seamless curricula which emphasize interdisciplinary nature of science in the 21st century and promote exploration, innovation and research. Normally, selected students will be accepted in the school of their choice, subject to availability of seats. At the end of the first year, a student will have an opportunity to change to another school, subject to availability of a seat in that school.

The curriculum for the first two semesters (first year) is common to all students and specialization begins from the third semester. The core courses in the subject of specialization provide strong foundations in both theoretical and experimental aspects of the discipline. Even after specialization in second year, students are required to go through a certain number of courses in other desciplines. All students are required to go through a small number of compulsory courses in humanities, technical communication, history of science, environmental and energy sciences.

The fourth year of the integrated M.Sc. Programme is devoted to advanced courses in various sub-disciplines. In the fifth year every student will undertake a guided research project. The outcome of the investigation will be reported in the form of a thesis. Throughout the five-year programme, students will be encouraged to take up summer projects and visit reputed national laboratories and universities. Eminent scientists from India and abroad will be regularly invited to give colloquia/seminars and interact with the students. In short the curricula are designed to ensure depth in the area of specialization together with breadth of exposure and intellectual enrichment and to prepare the students for high level professional research and development career in national laboratories, universities and industry.

The academic session for fresh students generally begins in August every year.