The clergyman from St Joseph's Church in Reddish, Greater Manchester was threatened with a screwdriver early on Tuesday morning by the two robbers.
They stole a laptop, watch and the priest's iPhone before forcing him to show them where donations were kept.
After locking him in a cupboard, they took the money and fled.
Police were alerted to the robbery at the priest's living quarters when two other priests that had hid in their rooms after hearing what was going phoned the emergency service.
Detective Constable Andrew Budsworth said: "This was a terrifying robbery where the offenders really are the lowest of the low. They knew that they were intending on stealing money that had been donated to charity.
"The victims were left incredibly shaken by their ordeal and we are doing all that we can to help them through it and get them the justice they deserve."
Anyone with any information is asked to call police on 0161 856 9970 ore alternatively call 101 or Crimestoppers anonymously on 0800 555 111.
