The priest, whose sentence may be suspended after two years, has also been banned from carrying out any professional activity that puts him in contact with minors.
The priest had admitted to one case of abuse in a letter in 2011 to the prosecutor of his home town in central France, Clermont-Ferrand.
But investigators had initially identified a total of four victims.
However they lost track of two of them in the chaos of the Central African Republic's civil war, which erupted in 2013.
When he set out for Central Africa in 2007, the priest said he wanted to build a hospital and to “fight sorcery”.
One of his victims was a 12-year-old orphan who told his friends — and then his headmaster — about his ordeal.
The priest then confessed his crimes in the Central African capital Bangui, and then to the archbishop of Clermont-Ferrand upon returning to France, before writing a letter to the prosecutor.
French troops backed by a UN mandate arrived in December 2013 in the Central African Republic, with a mandate to quell the violence there.
The French operation, which officially ended in October last year, was not entirely smooth, with its troops coming under intense pressure over allegations of child rape.
The Catholic hierarchy has also come under fire in recent years, with a string of historic paedophilia cases in North America and Europe unleashing widespread criticism.
Pope Francis issued a decree last year that senior Catholic officials guilty of negligence in child abuse cases can now be dismissed from office.
In January, he reiterated his stance, saying that the church's “zero tolerance” approach to abuse means just that.