Stephen Hopkins was baptized in 1581 at Upper Clatford, Hampshire, England. He sailed on Mayflower with his second wife Elizabeth Fisher, three children, and servants Edward Doty and Edward Lester. Elizabeth was pregnant when the voyage began, and she delivered a son while on board who she named Oceanus. The whole family survived the first winter, and Stephen and Elizabeth lived in Plymouth for 20 years.

In 1609, a Stephen Hopkins serving as a minister's clerk on the vessel Sea Venture was found guilty of fomenting a mutiny. He was sentenced to death for the crime, but granted a pardon due to his penitence and claims of ruin to wife and family. It has been suggested that this Stephen Hopkins was the same man as the Mayflower passenger, but this has not been proven.