Moville man Fr Eugene Boland, a parish priest in Killyclogher in County Tyrone, was forced to stand down from his role as parish priest after the false allegations were made.
He had to wait more than 18 months to be cleared by the Church after being found not guilty at a criminal trial in Derry.
He had returned to his parish two weeks ago.
The Donegal-born priest’s resignation was announced in a statement issued by the Diocese of Derry.
The statement said Fr Boland had been engaged in therapy sessions to prepare for his return to ministry after being cleared of the allegations of abuse.
However on his return it had “all too quickly become clear to Fr Boland and diocesan authorities that he is not ready.”
The statement said Fr Boland now needs more time for help and guidance in this regard, and has been granted leave of absence from ministry.