In spite of his primary residence in Philadelphia, Thomas McKean remained the effective leader for American independence in Delaware. Along with George Read and Caesar Rodney, he was one of Delaware's delegates to the First Continental Congress in 1774 and the Second Continental Congress in 1775 and 1776. Being an outspoken advocate of independence, McKean's was a key voice in persuading others to vote for a split with Great Britain. When Congress began debating a resolution of independence in June 1776, Caesar Rodney was absent. George Read was against independence, which meant that the Delaware delegation was split between McKean and Read and therefore could not vote in favor of independence. McKean requested that the absent Rodney ride all night from Dover to break the tie. After the vote in favor of independence on July 2, McKean participated in the debate over the wording of the official Declaration of Independence, which was approved on July 4.
A few days after McKean cast his vote, he left Congress to serve as colonel in command of the Fourth Battalion of the Pennsylvania Associators, a militia unit created by Benjamin Franklin in 1747. They joined Washington's defense of New York City at Perth Amboy, New Jersey. Being away, he was not available when most of the signers placed their signatures on the Declaration of Independence on August 2, 1776. Since his signature did not appear on the printed copy that was authenticated on January 17, 1777, it is assumed that he signed after that date, possibly as late as 1781.
In a conservative reaction against the advocates of American independence, the 1776/77 Delaware General Assembly did not reelect either McKean or Caesar Rodney to the Continental Congress in October 1776. However, the British occupation following the Battle of Brandywine swung opinions enough that McKean was returned to Congress in October 1777 by the 1777/78 Delaware General Assembly. He then served continuously until February 1, 1783. McKean helped draft the Articles of Confederation and voted for their adoption on March 1, 1781.
When poor health caused Samuel Huntington, to resign as President of Congress in July 1781, McKean was elected as his successor. He served from July 10, 1781, until November 4, 1781. The President of Congress was a mostly ceremonial position with no real authority, but the office did require McKean to handle a good deal of correspondence and sign official documents. During his time in office, Lord Cornwallis's British army surrendered at Yorktown, effectively ending the war.
McKean was over six feet tall, always wore a large cocked hat and carried a gold-headed cane. He was a man of quick temper and vigorous personality, "with a thin face, hawk's nose and hot eyes." John Adams described him as "one of the three men in the Continental Congress who appeared to me to see more clearly to the end of the business than any others in the body." McKean died in Philadelphia and was buried in the First Presbyterian Church Cemetery there. In 1843, his body was moved to the Laurel Hill Cemetery, also in Philadelphia. McKean County, Pennsylvania is named in his honor, as is Thomas McKean High School in New Castle County, also McKean Street in Philadelphia, and the McKean Hall dormitory at the University of Delaware. Penn State University also has a residence hall and a campus road named for him.