Atherton was born in 1598 in Somerset, England. He studied at Oxford University and joined the ranks of the Anglican clergy. In 1634 he became Bishop of Waterford and Lismore in the Church of Ireland. In 1640 Atherton was accused of buggery with a man, John Childe, his steward and titheproctor. They were tried under a law that Atherton himself had helped to institute. They were both condemned to death, and Atherton was executed in Stephen's Green, Dublin. Reportedly, he confessed to the crime immediately before his execution, although he had proclaimed his innocence before that. More recently, some historical evidence has been developed that shows Atherton might have been a victim of a conspiracy to discredit him and his patrons. This was attributable to Atherton's status as an astute lawyer, who sought to recover lost land for the relatively weak Protestant Church of Ireland during the 1630s. Unfortunately for Atherton, this alienated him from large landowners, who then allegedly used his sexuality to discredit him.
Posthumous accusations of sexual wrongdoing also include allegations of "incest" with his sister-in-law, and infanticide of the resultant child, as well as zoophilia with cattle. However, these allegations began to be circulated several months after his death in an anonymous pamphlet, and may have been intended to further discredit the bishop's campaign to restore the finances of the Church of Ireland