Recent biographies concur that John Abernathy was probably born in Bligh (near Cookstown), Co. Tyrone on 19th October 1680. His father, also John, was a Presbyterian minister there. In 1698 John Abernathy senior went to London with Patrick Adair to communicate Irish Presbyterian support for William III. His mother took refuge in Derry/Londonderry: John’s siblings were among the 10,000 who died in the famous siege. John had been sent instead to relatives in Ballymena who then brought him to Scotland where he was educated. In 1692 he returned to his parents in Coleraine. He went to Glasgow University aged 13, graduated MA in 1696, studied divinity in Edinburgh and returned to Ireland in 1701/2.
He was ordained in 1703 and became minister in Antrim. He married Susannah Jordan (d. 1712), with whom he had one son and three daughters.
Abernathy had a leading role in the Irish Presbyterian debate over whether ministers should be obliged to sign up to the Westminister Profession of Faith, an obligation only introduced in the Irish Presbyterian Church in 1705. The debate raged from 1719 until 1726, when the non-subscribing ministers, including John Abernathy, were sequestered in the Presbytery of Antrim.