Christopher Howarth, 68, abused the boy in question from 2005 to 2011 during his time at Holy Trinity Church in Uckfield, in East Sussex, and as deputy headteacher of Uckfield Community Technology College.
Mr Howarth had previously plead guilty in Hove Crown Court to two other counts of sexual abuse against another boy.
Police have said the Diocese of Chichester suspended Mr Howarth as soon as allegations he abused children came to light, and were fully compliant in their investigations.
Detective Constable Amy Green, from Sussex Police, said: "Howarth came to know the boys in his capacity as a lay priest at Holy Trinity CofE church in Uckfield, when they were very young, and befriended them over several years, giving support, but also offending against them. He was suspended by the Church as soon as the allegations came to light.
"Some of the offences against both boys took place in the study at his home, and one of the boys was also assaulted in Howarth's office at Uckfield Community Technology College, where he was deputy principal until his retirement eight years ago.
"The Diocese of Chichester and the College have given us full co-operation throughout this investigation.
"This illustrates once again the way in which we will always take seriously such allegations, refer victims to sources of support and counselling, and where appropriate will recommend prosecution."
Mr Howarth has been remanded in custody and will be sentenced on August 7th.
