The regiment suffered extensive casualties during the First Battle of Bull Run during the fighting on Henry House Hill and while serving as the rear guard for the retreating Union Army.

On April 15, 1861, President Lincoln issued an Executive Order calling for 75,000 ninety-day enlistments to "repossess the forts, places, and property which have been seized from the Union.

A national tour in 1860 brought Ellsworth to the attention of Abraham Lincoln, for whom the unit performed hundreds of military drill movements with their muskets and bayonets.

"[9] Two days after his arrival, Ellsworth awarded officer commissions to several foremen of the volunteer fire companies and began recruiting in earnest.

[10] When the state could not afford to supply the new troops, fundraisers were successful in raising $60,000 for the regiment, enough to provide uniforms, several different models of Sharps rifles, and provisions.

The men have been mustered into service; the officers elected; the uniforms made, and on Sunday afternoon eleven hundred as efficient and hardy soldiers as ever handled a gun, will start for the scene of rebellion.

John E. Wool, commander of the Department of the East, knew of the postponement, but allowed the men to embark, unaware the steamer Baltic carried no provisions.

[14] Quartermaster Arthur quickly purchased five-day rations, by paying a higher price, and hired three tug boats to catch the steamer to deliver them.

[17] The more embarrassing and lawbreaking actions by the regiment included the burning of fences, which resulted in a letter of reprimand from Brigadier General Joseph K. Mansfield along with six enlisted men being removed and sent back to New York.

Gen. Irvin McDowell on the East Front of the unfinished Capitol in the presence of Lincoln, his son Tad and personal secretary John Hay.

[20] Upon receiving word from General Mansfield, commander of the Department of Washington, Ellsworth dispatched ten men from each company to attend to the fire.

[23] While just five miles (8 km) from the capitol, the standard of living the men were used to had changed dramatically, as their usual foodstuffs were replaced with beef steak, dry bread, and coffee.

[25] On May 24, the regiment boarded the steamers Baltimore and Mount Vernon and was transported across the Potomac, landing at the Alexandria wharves under the guard of the gunboat Pawnee.

[29] Ellsworth's group entered the inn and quickly cut down the flag, but they encountered the proprietor, James Jackson, as they descended the stairs.

The 11th New York expected to first engage Confederates at Fairfax Court House on July 17, only to find that they had pulled back towards Centreville, leaving Quaker Guns in their place.

Poor scouting by Union chief engineer John G. Barnard resulted in a 14-mile (23 km) march for men entering battle that morning.

These units were ordered to support two batteries of cannon on the Federal right flank led by Captains Charles Griffin and James B. Ricketts.

The 11th New York and 1st Minnesota were directed into position at the top of Henry House Hill by Major William Farquhar Barry, McDowell's chief of artillery, and ordered to assault the Confederate line.

Stuart mistook the New Yorkers for retreating Confederates in the smoke and quickly rode forward, shouting, "Don't run, boys; we are here."

[41] Stuart ordered a small band of "Black Horse" cavalry, led by R. Welby Carter and the men of his Loudoun Company, to charge from the right and strike the 11th's rear guard.

[43] The 11th's volleys quickly killed eight of the riders and wounded nine with the rest escaping back into the woods; the charge had little effect on the organization of Fire Zouaves.

As the gunners confronted the blue-clad 33rd Virginia, Major Barry ordered Ricketts to hold his fire, allowing the Virginians to charge the batteries and capture the guns.

While the 14th Brooklyn was able to quickly retake the guns, the Union regiments supporting the cannon were unable to withstand the near constant barrage from Confederate artillery and infantry and fell back again to the Manassas-Sudley Road.

[48] On August 12, 1861, the remaining members of the regiment were sent back to New York City to disband, in preparation to reorganize, obtain equipment and replacements.

[49] On September 14, 1861, after reorganizing, they were ordered by Governor Edwin D. Morgan, at the request of Secretary of War Simon Cameron, to return to Virginia with two days' cooked rations.

[53] Initially intended to express anger at the draft, the protests deteriorated into "a virtual racial pogrom, with uncounted numbers of blacks murdered on the streets".

[54] The conditions in the city were such that Major General John E. Wool stated on July 16, "Martial law ought to be proclaimed, but I have not a sufficient force to enforce it".

[55] States' militias and Federal troops attached to the Army of the Potomac, including the newly reorganized 11th New York, were dispatched to quell the riots.

[66] Throughout its service, the regiment was armed with National Armory (NA) manufactured[note 3] model 1855 rifle-muskets drawn from state arsenals.

During their service, the 11th New York wore two different style of uniforms, the first issued during the forming of the regiment and the second shortly before the Battle of Bull Run.