Prime Minister Success Masra announced his candidacy for president one week after interim president Mahamat Deby, the head of the junta, announced his candidacy.
Mr Mathra, a former opposition leader, signed a settlement agreement with Mr Devi upon his return from exile before being appointed prime minister in January.
He told his supporters at a rally on Sunday that he was seeking the top position to unite people and “heal hearts.”
Opposition parties criticized the move as a ploy to create an impression of pluralism in an election that Deby was certain to win.
Max Kemkoe, a spokesman for the opposition GCAP, told AFP news agency that this was “a farce, a false candidacy to accompany the heads of military powers.”
Mr Deby’s main rival, opposition leader Yaya Dilo, was killed on February 28 in a gunfight with security forces.
The government had accused him of carrying out deadly attacks on security services, a charge he denied.
It was widely expected that he would be Mr Debbie’s main opponent in the election.
Mr Deby became Chad’s leader after his father, who had been in power for 30 years, was killed by rebels.