Father Daniel Doherty was spotted abusing the victim by fellow passengers travelling on the service to Edinburgh Waverley station.
After growing concerned, the witnesses contacted police and rail staff to report what they had seen before moving to a different carriage.
Train managers attended and questioned Doherty, who stated “we are just friends” and claimed that he had been “affirming” the victim.
During the conversation, the witnesses noticed that the 61-year-old's trouser button was undone, his belt was secured, and his trouser zip was halfway undone.
The two men were then met by British Transport Police officers after arriving at their destination station.
The victim, who had woken up several times while being touched by Doherty, did not disclose anything had happened to him due to the priest standing close by.
The accused was reported to the police by the victim two days later.
Doherty, of Falkirk, appeared at Kirkcaldy Sheriff Court on 22 October 2024 where he admitted sexually assaulting the victim on three separate occasions.
On 12 December 2024, he was sentenced to 16 months imprisonment. His name has been added to the sex offenders register for 10 years.
Helen Nisbet, Procurator Fiscal for Tayside, Central and Fife, said: “Daniel Doherty committed these serious sexual offences while holding a position of trust within his community.
“His predatory behaviour was brought to light thanks to the courage of the victim coming forward and reporting it to the authorities.
"Doherty has now been held accountable and we hope this prosecution makes clear that COPFS takes allegations of sexual offending seriously.”
Police Scotland Detective Inspector William Harley added: “This was a hugely distressing experience for Doherty’s victim.
“He will now have to face the consequences of these despicable actions. Crimes such as this will not be tolerated and will always be thoroughly investigated by Police Scotland.
“Anyone with any concerns or information can report them to police by calling 101 or calling Crimestoppers, where anonymity can be obtained, on 0800 555 111.”