Police have confirmed the death of David Kato but say they are investigating the circumstances.
Uganda's Rolling Stone newspaper published the photographs of several people it said were gay next to a headline reading "Hang them".
Homosexual acts are illegal in Uganda, with punishments of 14 years in prison.
An MP recently tried to increase the penalties to include the death sentence in some cases.
The BBC's Kevin Mwachiro says it is unclear whether the death is linked to the Rolling Stone campaign.
There has been a recent spate of "iron-bar killings" in Mukono, where Mr Kato lived, in which people have been assaulted with pieces of metal.
Witnesses have told the BBC that a man entered Mr Kato's home near Kampala, and beat him to death before leaving.
His Sexual Minorities Uganda (Smug) group said Mr Kato had been receiving death threats since his name, photograph and address were published by Rolling Stone last year.
Frank Mugisha, the group's executive director, told the BBC's Network Africa programme he was "devastated" on hearing the news from New York.
"He was killed by someone who came in his house with a hammer, meaning anyone else could be the next target."
Mr Mugisha said Mr Kato had recently been concerned about the threats he had received.
Human Rights Watch (HRW) has called for a swift investigation into his death.
"David Kato's death is a tragic loss to the human rights community," said HRW's Maria Burnett.
He had campaigned against the Anti-Homosexuality Bill, which appears to have been quietly dropped after provoking a storm of international criticism when it was mooted in 2009.
Following a complaint by Mr Kato and three others, a judge in November ordered Rolling Stone to stop publishing the photographs of people it said were homosexual, saying it contravened their right to privacy.
Several activists said they had been attacked after their photographs were published.
Mr Mugisha called on the Ugandan government to step up security for gay people.
"We're strongly asking every gay and lesbian and bisexual and transgender person in Uganda to watch out for their security … [they] should take extra caution."
Rolling Stone editor Giles Muhame told Reuters news agency he condemned the murder and that the paper had not wanted gays to be attacked.
"There has been a lot of crime, it may not be because he is gay," he said.
"We want the government to hang people who promote homosexuality, not for the public to attack them."
"Iron-bar killings" were common in Uganda when former leader Idi Amin was in power in the 1970s.
A rapid response police team has been sent to the area and several suspects have been arrested over the killings.