The area now known as New Haven was originally the home of a tribe of Native Americans, the Quinnipiack, who built their villages around the harbor. The Quinnipiack were distressed over the bands of Pequot and Mohawk tribes raiding their area. They agreed to sell the tribe's land to a company of Puritans who had sailed into the harbor and were led by John Davenport and Theophilus Eaton. In exchange the settlers pledged to protect the natives and to allow them to use the lands on the east side of the harbor.

In 1640 the settlement originally named Quinnipiac was renamed Newhaven. New Haven struggled for the next few years to build a strong commercial trade with the outside world but were overshadowed by Boston and New Amsterdam.

King Charles I of England was accused of treason and beheaded in 1649. His son, Charles II, became king in 1660 and sought vengeance against the men who had signed his father's death warrant. Two of the men, Colonel Edward Whalley and his son-in-law Colonel William Goffe fled to America in 1661. They were hidden by John Davenport in a cave on top of New Haven's West Rock. Later, they were joined by a third regicide, John Dixwell. The story of the three men has become an integral part of the history of New Haven, three of the city's streets are named after them.

New Haven was incorporated in 1784, the first mayor was Roger Sherman, one of the signers of the Declaration of Independence. The population of New Haven is 121,951 as stated by the 2001 statistics. New Haven is approximately 18.85 square miles.