It was first sent to Baltimore and then to Washington, D.C. Once there, it became part of the I Corps, Army of the Potomac, assigned to the 2nd Brigade, Second Division.

The regiment was issued .69 caliber muskets converted from flintlock to percussion; they carried these until the Siege of Petersburg when they received Springfield rifles.

After several months of garrison duty and railroad repair, the 90th was sent along with the rest of its division to the Shenandoah Valley to stop Major General T. J. Jackson's force, but did not get into any battles.

The chaplain of the regiment, Horatio Stockton Howell, was cruelly murdered on the steps of the Lutheran Church during the retreat.

Lyle was temporarily appointed to command of the 1st Brigade, with Sellers taking over the regiment.

The regiment lost heavily during the Overland Campaign, losing 124 out of 251 men at the Battle of the Wilderness and another hundred at Spotsylvania Court House.

At the Battle of Globe Tavern, Leech, Jacob Davis, and about 90 men were captured when the Confederates overran its position.