John married Mary Pierson in 1690 in Bucks County, Pennsylvania.
John had 8 children with his wife Mary Pierson: William Scarborough, Sarah Scarborough, Mary Scarborough, Susannah Scarborough, Elizabeth Scarborough, John Scarborough IV, Hannah Scarborough, and Robert Scarbury Scarborough.
John died in Solebury, Bucks Pennsylvania on January 27, 1727 at the age of 60.
John came to Pennsylvania with his father John Scarborough II in 1682 at the age of 15. In 1784, his father returned to England to bring back his mother, leaving John behind with friends. However, John Scarborough II never returned to America.
When John was 17 he ran away from the family friends he had been left with and is believed to have lived with Indians for roughly 5 years. When returning to the colonies he was used as an interpreter by William Penn and is believed to be instrumental in preventing an Indian War. He is believed to have been great friends of the Indians, and is said to have visited them on religious missions.