Dayton was born in Elizabethtown (now known as Elizabeth), New Jersey. He was the son of Elias Dayton, a merchant who was prominent in local politics and had served as a militia officer in the French and Indian War. He graduated from the local academy, run by Tapping Reeve and Francis Barber, where he was classmates with Alexander Hamilton. He then attended the College of New Jersey (now known as Princeton University). He left college in 1775 to fight in the Revolution, and received an honorary degree in 1776.

Dayton was 15 at the outbreak of the Revolutionary War in 1775 and served under his father (Elias) in the 3rd New Jersey Regiment as an ensign. On January 1, 1777, he was commissioned a lieutenant and served as paymaster. He saw Service under Washington, fighting in the battles of Brandywine Creek and Germantown. He remained with Washington at Valley Forge and helped push the British from their position in New Jersey into the safety of New York City. In October 1780, Dayton and an uncle were captured by Loyalists, who held them captive for the winter before releasing them in the following year. Dayton again served under his father in the New Jersey Brigade. On March 30, 1780, at age 19, he was promoted to the rank of captain and transferred to the 2nd New Jersey Regiment, where he took part in the Battle of Yorktown. The Revolutionary War pension records indicate that he served as Aide-de-Camp to General Sullivan on his expedition against the Indians from May 1 – November 30, 1779. On July 19, 1799, Dayton was offered a commission as Major General in the Provisional United States Army, but declined.

Dayton married Susan Williamson and had two daughters. Susan's Revolutionary War Pension Application W.6994 states that the marriage occurred on March 28, 1779. A supporting letter, written by Aaron Ogden, a captain in the New Jersey Brigade, states that he "was present at the marriage of the said Jonathan Dayton and Susan his wife; which marriage ceremony was performed by the Reverent Mr. Hoyt, a Presbyterian Clergyman... in the fore part of spring of the year seventeen hundred and seventy nine (1779) while the New Jersey Brigade lay at Elizabethtown in the Borough of Elizabeth and state of new Jersey."

After the war, Dayton studied law and created a practice, dividing his time between land speculation, law, and politics. After serving as a New Jersey delegate to the Continental Congress and Constitutional Convention (of which he was the youngest member, at age 26), he became a prominent Federalist legislator. He was a member of the New Jersey General Assembly in 1786–1787, and again in 1790, and served in the New Jersey Legislative Council (now the New Jersey Senate) in 1789.

Dayton was elected to the U.S. House of Representatives in 1789, but he did not take his seat until he was chosen again in 1791. He served as speaker for the Fourth and Fifth Congresses. Like most Federalists, he supported the fiscal policies of Alexander Hamilton, and he helped organize the suppression of the Whiskey Rebellion. He supported the Louisiana Purchase and opposed the repeal of the Judiciary Act of 1801.

The city of Dayton, Ohio, was named after Jonathan Dayton. While he never set foot in the area, he was a signatory to the Constitution and, at the time the city of Dayton was established in 1796, he owned (in partnership with Arthur St. Clair, James Wilkinson and Israel Ludlow) 250,000 acres (1,011 km²) in the Great Miami River basin.

After resuming his political career in New Jersey, Dayton died on October 9, 1824, in his hometown. He was interred in an unmarked grave that is now under the St. John's Episcopal Church in Elizabeth, which replaced an original church in 1860. Shortly before Dayton's death, Lafayette visited him, as reported in an obituary in the Columbian Centinel on October 20, 1824: "In New-Jersey, Hon. JONATHAN DAYTON, formerly Speaker of the House of Representatives of Congress, and a Hero of the Revolution. When the Nation's Guest lately passed New-Jersey, he passed the night with General Dayton, and such were the exertions of this aged and distinguished federalist, to honor the Guest, and gratify the wishes of his fellow citizens to see, that he sunk under them ; and expired, without regret, a few days after."