On 9/9/1775, John Pugh Williams was commissioned as a Captain under Col. Edward Vail, Sr. in the newly-created Edenton District Minutemen. All Minutemen regiments were disbanded on 4/10/1776.

On 4/16/1776, John Pugh Williams was commissioned as a Captain under Col. Edward Buncombe in the newly-created 5th NC Regiment on the Continental Line. He led his company at the battles of Brandywine Creek, PA (9/11/1777) and Germantown, PA (10/4/1777). His name was dropped from all official rolls in January of 1778, but it is not currently known when he resigned his commission.

Sometime in late 1778, John Pugh Williams was commissioned as a full Colonel, alongside Col. Thomas Pugh, in the Bertie County Regiment of Militia. There are hints that he might have only been a Lt. Colonel.

On 5/12/1779, John Pugh Williams was commissioned as a Brigadier General over the Edenton District Brigade of Militia, but he resigned three days later.

In July of 1780, Col. John Pugh Williams was assigned to the Staff of Maj. Gen. Richard Caswell, and both were at the battles of Little Lynches Creek, SC (8/11/1780) and Camden, SC (8/16/1780). It is assumed that Col. John Pugh Williams retired upon his return home from this battle.