Starkey was born in Bermuda, the first of at least five children of George Stirk, a Scottish minister and devoted Calvinist, and Elizabeth Painter. During his early years in Bermuda, Starkey displayed interest in natural history, as evidenced by his written entomological observations of various insects indigenous to Bermuda. After the death of his father in 1637, Starkey was sent to New England, where he continued his early education before enrolling at Harvard College in 1643 at the age of 15. Introduced to alchemical theory, he would later stylise himself as the "Philosopher by Fire." After graduating from Harvard in 1646, Starkey resided in the Boston area and earned a living practising medicine while at the same time experimenting in chemical technology.