Richard Franchot was appointed colonel of the regiment and authorized to establish his headquarters at Richfield Springs, Otsego County.

The 121st Regiment proceeded to Washington, arriving there on the morning of September 3, and was assigned provisionally to a brigade under Colonel Gibson with headquarters at Fort Lincoln.

On the march to the South Mountain and Antietam battlefields the regiment was assigned to the Second Brigade, First Division, Sixth Corps and remained with the command during its entire term of service.

Private Harris Hawthorn of the 121st New York claimed his capture and applied for and received the Medal of Honor for this act in the year 1894.

The 37th Massachusetts Infantry disputed this award in the year 1897, claiming that Private David Dunnels White of their regiment was the actual captor of Major General Custis Lee.