In early 1776 (or even as early as 1775), John Sheppard was commissioned as a Captain under Col. Abraham Sheppard (his father) in the Dobbs County Regiment of Militia. Capt. John Sheppard led his company at the battle of Moore's Creek Bridge on 2/27/1776.

In April of 1777, John Sheppard was commissioned as a Major under Col. James Glasgow in the Dobbs County Regiment of Militia, both promoted beccause Col. Abraham Sheppard was given command of the newly-created 10th NC Regiment on the Continental Line. In late 1778, he was a Major under Col. William Caswell, who had taken over the Dobbs County Regiment. Maj. John Sheppard and Col. William Caswell led the Dobbs County Regiment of Militia at the battle of Briar Creek, GA on 3/3/1779.

On 7/30/1779, John Sheppard was commissioned as a Lt. Colonel under Col. William Caswell in the Dobbs County Regiment of Militia, replacing Lt. Col. Henry Goodman, who resigned due to illness.

On 11/2/1779, the NC General Assembly created Wayne County from part of Dobbs County, and soon thereafter they commissioned John Sheppard as the second Colonel, alongside Col. Benjamin Exum, in the newly-created Wayne County Regiment of Militia. Both retained these positions until the end of the war (assumed, records incomplete).

Col. John Sheppard led the Wayne County Regiment of Militia at the Siege of Charleston, SC (3/28-5/12/1780). His regiment was stationed eight miles north of the city and was not captured when the town surrendered to the British on 5/12/1780.