Caius was born in Norwich and was educated at Norwich School. In 1529 he was admitted as a student at what was then Gonville Hall, Cambridge, founded by Edmund Gonville in 1348 - where he seems to have mainly studied divinity.
After graduating in 1533, he visited Italy, where he studied under the celebrated Montanus and Vesalius at Padua. In 1541 he took his degree as a physician at the University of Padua.
In 1543 he visited several parts of Italy, Germany and France and then returned to England. Upon his return from Italy he Latinised his surname, an action which although self-aggrandising, was somewhat fashionable at the time.