Police fired tear gas to disperse the crowd attacking a house in the Kalash tribe's valley of Bumburate in the northwestern district of Chitral, where the girl had gone to give a police statement about her conversion, said Kalash activist Luke Rehmat.
The Kalash, country's smallest religious minority, celebrate their gods through music and dance - an anomaly in conservative Muslim Pakistan.
Faces of Kalash: Untold stories of the valley
They number only around 4,000, according to Rehmat. Increasingly their youth are converting to Islam, prompting activists to campaign to preserve the traditions of the ancient, diminishing tribe.
The teenager had "returned to her home saying embracing Islam was a mistake and she wanted to live with her family, which infuriated the Muslim community," Rehmat said.
She went to a neighbour's house to speak to police, the home's owner told AFP, but hundreds of people began to gather outside as word spread through the close-knit community.
"The Kalash community had also gathered to save the family and when the Muslims chanting slogans attacked the house with sticks and pelted stones everybody was running for their lives," Rehmat, who was out of breath from fleeing the scene, told AFP by telephone.
"Dozens" were injured, he said, though apparently none seriously.
"Law enforcement agencies reached here on time otherwise they would have killed all of us," said local Kalash politician Imran Kabeer.
It was not clear what happened to the teenager.
Conversions threaten ancient Kalash tribe
Police of Chitral said the district police chief had gone to Bumburate with other senior officers, adding that the situation was under control.
The owner of the house that was attacked was also in Chitral, where he said police were refusing to let him return home.
"They came out in a mob to attack my house and to kill my wife and my children," he said, asking to remain anonymous.
"They threw stones at the roof and at the windows. Police were firing in the air."
Chitral, a northern district of Khyber-Pukhtunkwa, has long attracted tourists for its beauty and has hitherto been notable for having been spared the country's violence.
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