Science, technology, engineering and mathematics (STEM) education and research are globally recognised as engines of growth and development and indicators of citizens' well-being. Studies have continuously highlighted the unequal access and participation in STEM higher education based on class, caste, gender, disability and other markers of identity. This research paper investigates the underrepresentation of women in STEM at the Indian Institute of Technologies (IITs) in India. IITs are India's top elite institutions that open window of opportunities to students across the world. The study uses the data available from the All India Survey of Higher Education (AISHE), the Council of Indian Institute of Technology and the websites of the IITs. The findings indicate a significant gap between males and females in faculty positions at IITs. Furthermore, the study finds that the underrepresentation of women faculty differs across the STEM disciplines at IITs in India. It needs more gender-just affirmative action policies such as intersectional reservation for women in STEM academic careers, funding, legal protection against harassment, and representation of women in various committees and leadership positions.