Haskell was receiving his education in Heidelberg, Germany when he decided to return in 1861, and enlisted in the 14th New York Volunteer Infantry Regiment as a private. He fought at the First Battle of Bull Run where he sustained slight wounds and sunstroke. He later served as second Lieutenant Colonel in the 5th Missouri Volunteer Infantry and the 27th Missouri Volunteer Infantry building forts. He also served as an aide to General Alexander Asboth at the Battle of Pea Ridge and General Henry Prince at the Battle of Cedar Mountain (also known as Slaughter's Mountain), where he was severely wounded in the thigh by a minié ball. Haskell was the only member of General Prince's staff to escape with his life; he was hospitalized for four months after the battle.