He was charged with 39 counts of sexually assaulting the juvenile, who was aged between 11 and 17 at the time, on various dates between Jan 1, 1986, and Feb 22, 1994, at several locations.
Garda Caroline Keogh said Fr Mercer made no reply to the charges when they were put to him after caution.
Inspector Mary King told the court the Director of Public Prosecutions had directed trial by indictment before a judge and jury at circuit court level and that gardaí had no objection to bail with conditions attached.
Defence solicitor Robert Eagar said his client was willing to abide by the conditions including that he reside with the Dominican community at Black Abbey in Kilkenny where he lives.
Fr Mercer is also required to sign on twice weekly at Kilkenny Garda Station and not to have any contact directly or indirectly with children as part of his bail terms.
Judge Con O’Leary remanded Fr Mercer on his own bail of €2,500 to appear again at Cork District Court on Jan 10.