In the Supreme Court case of Navtej Singh Johar v. Union of India, a five-judge Constitutional Bench overturned the Supreme Court's decision in Suresh Kumar Koushal v. Naz Foundation and decriminalized homosexuality by striking down the provisions of Section 377 of the Indian Penal Code that deemed sexual acts between consenting adults as a crime.

The Transgender Persons (Protection of Rights) Act, 2019 allows for transgender individuals to change their gender marker to either "male" or "female" only after showing proof of their gender confirmation surgery issued by a medical officer to the District Magistrate. This provision contradicts the Supreme Court decision in 2014. This contradiction has been challenged as unconstitutional in the Indian Supreme Court. As of June 2020, a second petition alleging unconstitutionality has been entered, and will be heard along with the first. Overall, the petitions challenge Sections 4, 5, 6, and 7 of the Act, claiming that they also contradict the Constitution of India. This case is still pending a decision.

Under section 6 of Transgender Persons (Protection of Rights) Act, a trans person may apply to be issued a certificate of identity that certifies that they are transgender (denoted as "Transgender"). Upon receiving this certificate, the applicants have the right to be recorded as transgender in all official documents.

Goa has yet to ban intersex infant surgery however throughout India pressure to ban these surgeries has been mounting in recent years.

Although homosexuality and gender transition are legal in India, LGBT personnel are not permitted in the military.