Riyaz Naikoo had taken over command of the banned Hizbul Mujahideen group, succeeding Burhan Wani who was killed by security forces in 2016.
Wani’s death triggered massive protests in the region, which is claimed in its entirety by both India and Pakistan.
The region has seen an armed insurgency against Indian rule since 1989, which has flared following Wani’s killing.
Naikoo was shot dead in his home village of Beigh Pora in Pulwama district after militants killed eight security personnel in two separate attacks, part of a recent surge of violence in Indian-administered Kashmir.
Locals said the militant leader had been trapped in a joint siege laid by army, paramilitary and police forces. He had been on the run for eight years.
“At least 76 militants including Naikoo have been killed since January this year. But we also lost 20 soldiers including senior army and police officers,” a security official told BBC Urdu on condition of anonymity.
Under a new policy, militants who are killed are not identified and their bodies are not handed over to their families.
Officials had accused Riyaz Naikoo of plotting attacks against the security establishment in the valley.
Disputed Kashmir has been a flashpoint for more than 60 years, sparking two wars between India and Pakistan.
In August 2019, the Indian government stripped the region of its semi-autonomous status and split it into two federally-run territories.
Thousands of people were detained and the region remains under severe security restrictions.