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John Newton (junior) was born in Wapping, London, the son of John Newton, a shipmaster in the Mediterranean service, and Elizabeth Newton (née Seatclife). His mother brought him up as a Nonconformist Christian. She died of tuberculosis when he was 6. Newton spent 2 years at boarding school, at the age of 11 he went to sea with his father and sailed with him on a total of six voyages until the elder Newton retired in 1742. Newton's father had planned for him to take up a position as a slave master at a sugar plantation in Jamaica but in 1743, he was pressed into naval service, and became a midshipman aboard HMS Harwich. After attempting to desert, Newton was put in irons and court martialed. The captain was determined to make an example of Newton for the rest of the crew. Thus, in the presence of 350 members of the crew, the 19-year old midshipman was stripped to the waist, tied to the grating, and received a flogging of eight dozen lashes, and was reduced to the rank of a common seaman. Following that disgrace and humiliation, Newton initially contemplated suicide, but he recovered, both physically and mentally, and, at his own request, he was placed in service on a slave ship bound for West Africa which eventually took him to the coast of Sierra Leone. He became the servant of a slave trader, who abused him. It was this period that Newton later remembered as the time he was "once an infidel and libertine, a servant of slaves in Africa." Early in 1748 he was rescued by a sea captain who had been asked by Newton's father to search for him on his next voyage.

Sailing back to England in 1748 aboard the slave-ship Greyhound on the Atlantic triangle trade route, the ship encountered a severe storm and almost sank. Newton awoke in the middle of the night and prayed to God as the ship filled with water. It was this experience which he later marked as the beginnings of his conversion to evangelical Christianity. As the ship sailed home, Newton began to read the Bible and other religious literature. By the time he reached Britain, he had accepted the doctrines of Christianity. The date was March 10, 1748, an anniversary he marked for the rest of his life. From that point on, he avoided profanity, gambling, and drinking, although he continued to work in the slave trade. He later said that his true conversion did not happen until some time later: "I cannot consider myself to have been a believer in the full sense of the word, until a considerable time afterwards."