Jume Tahir, who is also vice-president of the China Islamic Association, was stabbed to death outside the ancient mosque.
The indictment comes amid unending violence in China's restive western Xinjiang region.
Officials say they were targeted after he led a raid on a mosque prayer session.
At least two sources say the death toll may have exceeded 50 but the information cannot be officially verified.
A State Department report hits out at religious controls in China.
The Uyghurs are ordered imprisoned between six months and seven years after a hushed-up trial.
Residents say discriminatory policies provoked the incident.
Police kill one Uyghur suspect and detain three others in the latest violence in the restive region.
The officer had recently been tasked to run an anti-terror campaign in the region.
College administrators distribute bottles of water and offer free lunches to students during Ramadan, and those who refuse are blacklisted.
Uyghurs are also being denied access to accommodation in Beijing, local rights activists say.
Authorities say he led a group that planned police station attacks.
He had spoken out in support of a longtime advocate for Uyghur rights.
Gas stations are banned from selling petrol in canisters, by police order.