Roger Toothaker was born in England in 1634. In 1635, as an infant, Toothaker traveled to the Massachusetts Bay Colony from London, sailing from August 21 to September 11 on the Hopewell, led by Captain Babb. In 1638, his father, Roger Toothaker, died, possibly in Plymouth on February 5. Later that year his mother Margaret married Ralph Hill on December 21 and they lived in Billerica. He served as an assistant to Samuel Eldred, and later became a physician although he had no formal medical training. Around 1662 to 1663 his stepfather Ralph Hill died. In 1665 he married Mary Allin and had nine children: Nathaniel, Martha, Allin, Roger, Sarah, Mary, Mary, Andrew, and Margaret.
Dr. Toothaker claimed to many people that his daughter, Martha, had killed a witch. On May 18, 1692, Elizabeth Hubbard, Ann Putnam, Jr., and Mary Walcott accused Dr. Toothaker of witchcraft. Elizabeth was the servant of Dr. William Griggs, Dr. Toothaker's competitor. On May 28, Mary Toothaker, Margaret Toothaker (aged 9), Martha Carrier, and Elizabeth Jackson were arrested. John Willard of Salem, Thomas Farrar of Lynn, and Elizabeth Hart were arrested along with Dr. Toothaker. Dr. Toothaker was sent to Boston Prison where he remained until his death in June 1692. His body was examined and it was confirmed that he died of natural causes, although it is impossible to separate his death from his imprisonment, and likely maltreatment and/or malnourishment.