Allen gained military experience during the Seven Years War, but he first rose to prominence as the commander of the Green Mountain Boys, a militia group first raised in 1770 to fight a Sheriff's party from New York. As a result of his actions, there was a price on his head in New York. When the fighting broke out in 1775, many Americans worried about Fort Ticonderoga on the western side of Lake Champlain. Originally a French stronghold it had been captured by the British in 1759. At the time it was a strong fortification, but by 1775 it had been allowed to crumble. However, it worried many Americans, and soon after Lexington Allen was approached by a group from Connecticut who offered to back him in an attack on Ticonderoga. Allen agreed, and raised a force of two hundred men, mostly Green Mountain Boys. At the same time Benedict Arnold had gained a commission from Massachusetts to attack the fort, but when he reached Allen and his men they refused to follow him. Eventually the attack went ahead with both men claiming command.
The attack itself was launched early in the morning on 10 May 1775, and is considered to be the first offensive action taken by American troops during the war. The British garrison was only fifty strong, and was surprised in its beds. This exploit made Allen and the Green Mountain Boys popular heroes in New York. His disagreements with Arnold continued. Arnold captured St. Johns on the Richelieu River, before abandoning it. Allen disagreed with this, and reoccupied St. John before himself being forced to abandon it by a British attack.
Nearly two months passed after the fall of Ticonderoga before Congress decided to launch an invasion of Canada. On 27 June General Philip Schuyler was appointed to command the invasion. Allen was sent to Canada to recruit, but instead found the Loyalists to be stronger. On 25 September he launched an attack on Montreal, but the Loyalists defeated his attack, and Allen was himself captured.
He remained in British captivity for nearly three years, before finally being released on 6 May 1778 in exchange for Archibald Campbell. He did not return to active service after his release, but instead returned to Vermont, which in 1777 had declared itself to be an independent republic. Allen campaigned in favour of this and against domination from New York even preferring annexation to Canada. He died in 1789, two years before Vermont joined the Union as the 14th state (1791)