The elder Cudworth died in 1624, when Ralph was seven. His mother remarried to a man named John Stoughton, who was also a committed Calvinist. Dr. Stoughton took charge of young Ralph's education, and did so with “great care,” making sure that by the time Ralph was thirteen “he was as well grounded in school learning as any boy of his age that went to University” (Birch viii). When he was fifteen, Cudworth was sent to Emmanuel College in Cambridge, where Stoughton himself had gone and was well connected.

This choice of college is significant. Emmanuel had been founded in 1584 by an early English Calvinist named Walter Mildmay with the express intention of preparing young men for the ministry. And by the time Cudworth arrived in 1632, the college had earned a reputation as the prime training ground for Calvinist preachers. Clearly, Stoughton's idea was to groom Cudworth to don the mantle that Perkins had worn and then passed to Cudworth's father. Ralph was a brilliant young man of impeccable background – just the person to carry forward the godly message of English Calvinism.

But it didn't happen. Although Cudworth remained politically and socially associated with the Calvinists for years to come, he quickly became one of the leading lights of a philosophical movement that was diametrically opposed to Calvinism's fundamental tenets.