Optical engineering programme is offered to prepare students for the application of fundamental optics in modern technology and research environments. Optics based applications abound in modern day technology, from space technology to applications in household gadgets such as laptops and PCs, and thus, optical engineering is an essential tool in majority of day to day applications. Moreover, the recent advent of quantum information technology is largely driven by a combination of fundamental optics and optical technology.

The M.Tech. in Machine Learning & Computing is a two-year postgraduate program offered by the Department of Mathematics, IIST, launched in 2010. It was one of the institute’s earliest master's programs and has grown to become one of its most sought-after offerings.

The M.Tech in Geoinformatics program at IIST, Thiruvananthapuram, is a rigorous two-year postgraduate course that equips students with a strong foundation in remote sensing, GIS, image processing, and geospatial data analysis. The curriculum blends methodological, computational, and technical aspects of Geoinformatics with practical training in modern data acquisition and advanced processing techniques.

The M.Tech.in Earth System Science is a two-year postgraduate programme that focuses on the study of the Earth’s atmosphere, oceans, and solid Earth. It aims to provide a comprehensive understanding of the dynamic processes that govern the Earth's climate and geophysical systems.The programme blends core concepts from atmospheric science, oceanography, and geology with quantitative methods and modeling tools. Key areas of study include atmospheric dynamics, physical oceanography, geophysical fluid dynamics, and Earth surface processes.

The Master of Science in Astronomy and Astrophysics is a two-year program offered to both dual degree students and those seeking direct admission to the post-graduate program at IIST. The first year focuses on foundational courses in astrophysics, along with hands-on training in astronomical observations and data analysis. The second year is dedicated to a thesis project in an area related to astronomy and astrophysics. The program aims to provide students with a strong academic and research foundation, preparing them for advanced studies and careers in astronomy and space science.

In the Dual Degree programme the student receives a B.Tech.degree in Engineering Physics and Master of Science / Master of Technology in one of the following four streams at the end of ten semesters -

M.Tech in Materials Science and Technology is a two-year postgraduate programme open to students from both science and engineering backgrounds. The curriculum is designed to provide a strong foundation in the fundamentals of materials science along with their diverse applications, including aerospace, semiconductors, sensors, energy storage, environmental applications, biomaterials, high-temperature systems, and computational materials science. Students will gain hands-on experience with advanced equipment used for materials characterization.

M.Tech in Power Electronics is a 2-year postgraduate program focused on advanced studies in the design, analysis, modelling, and control of power electronic systems. The courses included in this program cover Advanced Switched Mode Power Converters (AC-DC, DC-DC, DC-AC), Power Semiconductor Devices, Grid-Connected Systems, Control of Electric Drives and Digital Signal Processing (DSP) for Power Electronics, and Embedded Systems in Power Electronics, among others.

M.Tech in Control Systems at IIST is a unique two-year interdisciplinary Masters program aimed at providing due weightage to higher academic studies, R&D, as well as Industrial sectors. This well-structured and focused M.Tech programme, in line with ISRO’s missions and visions, gives a comprehensive exposure to the students in a wide area of systems, control, and computing theory and practice.