A seven-member jury returned a unanimous guilty verdict.
On December 30, 2018, Reverend Nabegmado was fatally stabbed at his church premises during service.
Francis reportedly bought a double-edged knife to carry out the attack.
He pushed the pastor against a wall upon entering his office and stabbed him multiple times.
Francis later blamed his actions on the influence of spirits, telling the court he wished to see his family and serve his sentence in Yendi.
In his defense, he denied committing the crime, claiming his hands were clean and that it was the spirit of the gods that killed the deceased.
His lawyers pleaded insanity, but a psychiatric evaluation at Pantang Hospital declared him fit to stand trial.
The trial began in 2022 after a jury was constituted.
Senior State Attorney Frederick Adu Gyamfi led the prosecution, calling six witnesses, while the accused presented one defense witness.
The prosecution said the complainant, Deacon Felix Nyarko, was a member of the church.
The deceased, head pastor of Central Assemblies of God Church, was his uncle.
Francis, who lived with the pastor, entered his office and attacked him while he was in a meeting.
A witness in the room ran out and raised an alarm.
Francis, holding a blood-stained knife, threatened to stab anyone who approached.
He scaled a wall and fled but was apprehended by a police officer who had just closed from work.
Police found him carrying a half bottle of Kasapreko gin, turpentine, a cutlass, and a knife.
Reverend Emmanuel Kwasi Ofori, the current head pastor, told journalists the church had been awaiting closure on the case and would release an official statement soon.
GNA