The Reverend Graham Buttanshaw, vicar of All Saints Parish Church in Otley, West Yorkshire, will now have to send his son Timothy to a non-church school.
Mr Buttanshaw wanted his three-year-old son to go in September to All Saints Church of England primary, where he is the parish vicar and sometimes takes assembly. But instead he was allocated to Westgate primary because the family live 0.9km from All Saints but only 0.4km from Westgate.
Mr Buttanshaw spoke of his shock at the decision, telling the BBC: "If the vicar can't get his child to the local church school then surely something must be wrong."
He later told The TES that he would not appeal against the ruling. "My son is going to another school," he said.
"We are happy that it is an excellent school."
A spokeswoman for Education Leeds, which made the decision, said: "School places across Leeds have to be allocated in line with our admissions policy, which requires that we treat every application equally."
All Saints had an admission limit of 30 pupils. Eleven pupils were allocated places because they had a sibling at the school. The other 19 were given to those who lived nearest to the school.
Jan Gasper, the headteacher of All Saints primary, said: "Of course we are disappointed at the decision. Timothy is with us in the nursery. He is a delightful child and we had anticipated him joining us in the main school."