Jean Uwinkindi organised and participated in attacks on the minority Tutsi ethnic group, the court ruled.
Some 800,000 Tutsis and moderate Hutus were killed by militias from the majority Hutu ethnic group.
The 64-year-old Hutu pastor was the first genocide suspect to be sent back to Rwanda for trial by the Tanzanian-based UN tribunal.
The tribunal shut down this month after sentencing 61 individuals and acquitting 14 others.
Uwinkindi - the former head of a Pentecostal church on the outskirts of the capital, Kigali - had opposed his transfer.
He said he would not get a fair trial in Rwanda, where there is now a Tutsi-led government.
His lawyers said he would appeal against the High Court's ruling.
"The court finds that there were killings of the Tutsi at Rwankeri and Kanzenze hills and that the attacks were led by Uwinkindi," said Judge Kanyegeri Timothee, Reuters news agency reports.
The prosecution alleged that in investigations after the genocide, some 2,000 bodies were found near the church in Kanzenze, just outside Kigali, where Uwinkindi was pastor.
He was indicted in 2011 after he was arrested in 2010 in neighbouring Uganda.
Another key suspect, Ladislas Ntaganzwa, who has a $5m (Â£3.2m) US bounty on him, was arrested two weeks ago in neighbouring Democratic Republic of Congo.
Rwanda's High Court has sentenced a pastor to life in prison for his role in the 1994 genocide.