Gage received a letter from Lord Dartmouth on April 14, 1775, advising him "to arrest the principal actors and abettors in the Provincial Congress whose proceedings appear in every light to be acts of treason and rebellion". On the night of April 18, Gage sent out a detachment of soldiers on the fateful mission that would spark the American Revolutionary War. The purpose of the British expedition was to seize and destroy military supplies that the colonists had stored in Concord. According to many historical accounts, Gage also instructed his men to arrest Hancock and Adams; if so, the written orders issued by Gage made no mention of arresting the Patriot leaders. Gage apparently decided that he had nothing to gain by arresting Hancock and Adams, since other leaders would simply take their place, and the British would be portrayed as the aggressors.
With the war underway, Hancock made his way to the Continental Congress in Philadelphia with the other Massachusetts delegates. On May 24, 1775, he was unanimously elected President of the Continental Congress, succeeding Peyton Randolph after Henry Middleton declined the nomination. Hancock was a good choice for president for several reasons. He was experienced, having often presided over legislative bodies and town meetings in Massachusetts. His wealth and social standing inspired the confidence of moderate delegates, while his association with Boston radicals made him acceptable to other radicals. His position was somewhat ambiguous because the role of the president was not fully defined, and it was not clear if Randolph had resigned or was on a leave of absence. Like other presidents of Congress, Hancock's authority was mostly limited to that of a presiding officer. He also had to handle a great deal of official correspondence, and he found it necessary to hire clerks at his own expense to help with the paperwork.
In Congress on June 15, 1775, Massachusetts delegate John Adams nominated George Washington as commander-in-chief of the army then gathered around Boston. Years later, Adams wrote that Hancock had shown great disappointment at not getting the command for himself. This brief comment from 1801 is the only source for the oft-cited claim that Hancock sought to become commander-in-chief. In the early 20th century, historian James Truslow Adams wrote that the incident initiated a lifelong estrangement between Hancock and Washington, but some subsequent historians have expressed doubt that the incident, or the estrangement, ever occurred. According to historian Donald Proctor, "There is no contemporary evidence that Hancock harbored ambitions to be named commander-in-chief. Quite the contrary." Hancock and Washington maintained a good relationship after the alleged incident, and in 1778 Hancock named his only son John George Washington Hancock. Hancock admired and supported General Washington, even though Washington politely declined Hancock's request for a military appointment.
When Congress recessed on August 1, 1775, Hancock took the opportunity to wed his fiancée, Dorothy "Dolly" Quincy. The couple was married on August 28 in Fairfield, Connecticut. John and Dorothy would have two children, neither of whom survived to adulthood. Their daughter Lydia Henchman Hancock was born in 1776 and died ten months later. Their son John was born in 1778 and died in 1787 after suffering a head injury while ice skating.