Following President Abraham Lincoln's call for 75,000 volunteers to put down the rebellion, Stainrook enlisted on April 23, 1861 in the Union Army as the captain of Company C of the 22nd Pennsylvania Infantry, a three-month regiment.

[2] Subsequently, Stainrook was involved in organizing the 109th Pennsylvania Infantry and was commissioned its colonel with a nominal date of November 1, 1861.

Stainrook was wounded in the abdomen by a shell fragment at the Battle of Cedar Mountain during the Northern Virginia Campaign.

Stainrook's brigade, after some confusion in deploying, passed through the East Woods, driving away the remains of the division of Brig.

The brigade moved along the axis of the Smoketown Road and reached the high ground at the Dunker Church.

Once Maj. Gen. John Sedgwick's division of the II Corps had been driven from the West Woods, Greene was forced to retreat.

[1] When Maj. Gen. Joseph Hooker undertook the Chancellorsville Campaign in the spring of 1863, Stainrook's regiment was in the brigade of Brig.

Stainrook commanded the brigade's skirmish line on May 1 near Hazel Grove, facing southward.

On May 3 and 4 XII Corps was positioned near the Chancellorsville House, receiving heavy fire from Confederate troops.