During the Civil War, Whaley was major of the 9th West Virginia Volunteer Infantry and captured during a Confederate raid, but escaped his captors.

During the Civil War, Whaley recruited men for the Union Army.

Commissioned as major of the 9th West Virginia Volunteer Infantry Regiment, Whaley was captured by Confederate forces under the command of General Albert Gallatin Jenkins on November 10, 1861, during a Confederate raid on the town of Guyandotte, West Virginia (now a neighborhood of Huntington, West Virginia).

He served on the Congressional committee that accompanied the body of President Abraham Lincoln on the funeral train as it was returned from Washington to Springfield.

[1] He did not seek reelection in 1866, and was replaced by fellow Republican Daniel Polsley.