Born near Bridgewater in Somerset, the son of an Anglican parson, Atherton was educated at Oxford. He served as Anglican rector of Huish Comb Flower, Somerset; and bevame prebendary of St John's, Dublin, in 1630. In 1636, he was appoitntes as Lord Bishop of Waterford and Lismore.

In 1640 he was accused of buggery with his steward and tithe proctor, John Childe. Though his fellow clerics tried to prevent the trial so as to avoid disgra to the reformed religion of Ireland, the verdict of guilty was hailed by cheers in court, and he was nearly murdered on his way from the bar to the gaol in Cork.

In court he denied the specific charge of sodomy, and did so one again from the gallows, though he admitted his guilt to the divine who attended him in prison. On December 5 he was hanged on Gallows Green of Dublin Castle. His lover, Childe, was hanged in March 1641 at Bandon bridge, Cork.