He was the only son of James Bathe, Chief Baron of the Irish Exchequer (died 1570) and his second wife Elizabeth, daughter of John Burnell of Balgriffin, and widow of Robert Barnewall of Drimnagh.
Despite some suspicions about his loyalty during the Rebellion of Silken Thomas, the elder Bathe became a trusted servant of the English Crown who held high judicial office for 30 years.
An earlier John Bathe, who held office as Chief Justice of the Irish Common Pleas 1554-9, was a cousin.
John was studying law at Lincoln's Inn in 1560, with the help of the legacy from his cousin Richard Burnell, and was called to the Bar there.
In 1576 he was appointed to a powerful royal commission to inquire into "concealed lands" in several counties, formerly held by monasteries and attainted persons.
Jenet and Warren are generally believed to have arranged Hugh O'Neill's much-discussed third marriage to Mabel Bagenal, which took place at Drumcondra Castle in 1591.