Shujaat Bukhari, the editor of Rising Kashmir newspaper, was shot as he was leaving the paper's office in his car in downtown Srinagar, the capital of Kashmir, on Thursday.
He was taken to hospital but was later declared dead, Presstv Reported.
One of his bodyguards was also killed and another critically injured in the attack, according to regional police.
So far, there has been no claim of responsibility but police suspect militants to have carried out the attack.
Bukhari was a well-known journalist and had been given round-the-clock security protection in the disputed Himalayan region, where journalists are constantly threatened.
The attack occurred only hours after he posted a tweet about the United Nations recent call for an investigation into alleged human rights abuses in the Muslim-majority region.
"First-ever @UNHumanRights report on #Kashmir calls for #international inquiry into multiple violations,” Bukhari tweeted on Thursday.
In another tweet, he wrote, “In #Kashmir we have done Journalism with pride and will continue to highlight what happens on ground."
Earlier on Thursday, the UN High Commissioner for Human Rights Zeid Ra’ad al-Hussein urged “the UN Human Rights Council to consider establishing a commission of inquiry to conduct a comprehensive independent international investigation into allegations of human rights violations in Kashmir.”
“It is a conflict that has robbed millions of their basic human rights and continues to this day to inflict untold suffering," he added.
New Delhi and Islamabad both claim the Himalayan region in full, but rule parts of it. Pakistan administers one-third of Kashmir, with the remaining two-thirds under India’s control.
The two nuclear powers have fought four wars, three of them over Kashmir.
Pro-independence activists in Kashmir have waged a campaign against Indian rule since the 1980s. Thousands of people have been killed in the unrest over the past decades.