Fr Peter Hannah was left "extremely shaken" after three men, one with a handgun, demanded him to empty the church safe at about 6.25pm on Tuesday.
The gang rang the doorbell at St Vincent de Paul Church in Derbyshire Hill Road before making off with cash that was to be given to a children's orphanage.
Merseyside Police said the priest was not assaulted or injured during the incident but was left extremely shaken.
Officers carried out an extensive search of the area but were unable to trace the three men.
Detectives say they are examining CCTV in the area and the men are described as white, with two of the men taller than the third.
All three had their faces covered and were described as being aged between 17 and 21.
Detective Sergeant Chris Burrows, from St Helens CID, said: "I am sure the people of St Helens will be shocked and saddened to discover the church has been targeted in this way.
"It is a focal point for many in our community, particularly at this time of year, and it is heart-breaking to think the offenders have taken money which we understand was a charitable collection intended for a children's orphanage.
"While he was thankfully not injured this would have been a very frightening incident for the priest.
"I would like to reassure people who live locally that we are doing everything we can to trace the offenders.
"Religious leaders provide an invaluable service in our local communities and I would urge anyone who lives locally and has any information which could help us with our inquiries to call us."
Anyone with information should contact detectives at St Helens CID on 0151 777 6811, or Crimestoppers on 0800 555 111.
