The incident happened on Tuesday at St John and St Columba's Church in Rosyth.
Police Scotland said they were investigating the incident.
Last July, a visiting priest in Broxburn, West Lothian, called in police after both he and parishioners were subjected to anti-Catholic chants by youths standing outside a church.
Police also had to be called in May 2015 after St Andrew's parish in Livingston was extensively spray-painted with anti-Catholic graffiti.
Father Kevin Dow, St John and St Columba's church priest, said: "It's dreadfully sad that in today's Scotland we still have young people who seem to be brought up or encouraged from elsewhere to be anti-Catholic and to do so in an open, intimidating and violent way."
A Police Scotland spokeswoman said: "Police in Fife received a report of a disturbance outside St John's Church in Rosyth on the evening of Tuesday 17th January.
"Officers are following a positive line of inquiry."
http://www.bbc.com/news/uk-scotland-edinburgh-east-fife-38680019