Higher education in India faces several challenges affecting quality, equity, access, and relevance. A low gross enrolment ratio (GER) is one of the major challenges. India's GER of 27.1 per cent in 2019-20 is below the global average of 38 per cent and much lower than that of developed countries. It also varies widely across states, gender, and social groups.

Many higher education institutions, especially those run by the public sector, suffer from inadequate physical facilities, outdated equipment, insufficient library and laboratory resources, and lack of internet connectivity. Besides, many institutions have a shortage of qualified and competent faculty members, leading to high student-teacher ratios and low academic standards. The quality and quantity of research output is also low compared to other countries, as reflected by the low citation impact and innovation index of Indian publications.

Lack of autonomy and accountability is a major challenge before the Higher education system. Higher education institutions are often subject to excessive regulation and interference by various authorities, which hampers their academic freedom and innovation. There is also a lack of transparency and accountability in governance, funding, accreditation, and assessment of institutions. Moreover, India has a low share of international students and faculty and low participation in global rankings and networks. The curriculum and pedagogy of many institutions are not aligned with the changing needs and expectations of employers and society, resulting in a skills gap and low employability of graduates.