In 1862 he was made Acting Assistant Surgeon, 5th PA Cavalry, U.S. Army and returned to Philadelphia as the Executive Officer of the Broad and Cherry Streets Hospital.

Except for a brief tour of duty in the Fort Sumter area, Yarrow served at this hospital until the end of the Civil War.

In 1872, Yarrow received an offer to join Lt. George Wheeler's explorations into the West of the 100th Meridian as surgeon and naturalist.

While on duty he prepared for publication a volume of zoology and made observations relating to a mono graph he would go on to publish years later - Introduction to the Study of Mortuary Customs among North American Indians.

In 1879, Henry Yarrow reported to Surgeon John Shaw Billings as an assistant on the Medical Index Catalogue project.

He died from heart disease at the Chamberlin-Vanderbilt Hotel in Hampton, Virginia on July 2, 1929, and was buried at Arlington National Cemetery.