He was the eldest son of John Marlowe of the Shoemaker's Guild and Katherine Arthur, a Dover girl of yeoman stock (Henderson 275). .
Upon graduating King's School, Canterbury, he received a six-year scholarship to Cambridge upon the condition that he studies for the church. He went to Cambridge, but had to be reviewed by the Privy Council before the university could award him his M.A. degree because of his supposed abandonment of going to church. He was awarded his degree in July of 1587 at the age of twenty-three after the Privy Council had convinced Cambridge authorities that he had "behaved himself orderly and discreetly whereby he had done Her Majesty good service- (Henderson 276). After this, he completed his education from Cambridge over a period of six years. During this time he wrote some plays, including Hero and Leander, along with translating others, such as Ovid's Amores and Book I of Lucan's Pharsalia (Henderson 276). During the next five years he lived in London where he wrote and produced some of his plays and traveled a great deal on government commissions, something that he had done while trying to earn his M.A. degree. In 1589, however, he was imprisoned for taking part in a street fight in which a man was killed; later he was discharged with a warning to keep the peace (Henderson 276). He failed to do so; three years later he was summoned to court for assaulting two Shoreditch constables, although there is no knowledge on whether or not he answered these charges (Henderson 276). Later Marlowe was suspected of being involved in the siege of Roven where troops were sent to contain some Protestants who were causing unrest in spite of the Catholic League. Then, after sharing a room with a fellow writer Thomas Kyd, he was accused by Kyd for having heretical papers which "denied the deity of Jesus Christ- (Discovering Christopher Marlowe 2). Finally, a certain Richard Baines accused him of being an atheist.