In 1776, McJunkin volunteered in Col. John Thompson's Fair Forest Militia Regiment, where he engaged in the Cherokee campaign. In May, 1777, he was made Captain and commanded at Fort Jamieson. He served a three month guard tour in Charleston, South Carolina, from November 1779 to February 1780. After the fall of Charleston, and the Battle of Camden, the Tory and Whig Militias engaged in guerilla war leading up to Huck's Defeat, and the Battle of King's Mountain.