He served primarily in the 15th Infantry Regiment and was assigned to several posts in the western United States during the American Indian Wars.

During the Spanish–American War he was assigned as mustering officer for volunteer soldiers being discharged at the end of their enlistments, and was posted to Washington, D.C., Georgia, and South Carolina.

During the post-war United States Military Government in Cuba, McGunnegle was an assistant inspector general on the staff of governor Leonard Wood.

[4] In August 1873, Grant nominated McGunnegle for a direct commission in the United States Army, and he received appointment as a second lieutenant.

[12] In March 1888, McGunnegle was serving as adjutant of the 15th Infantry at Fort Buford, Dakota Territory when the quarters in which he resided with the regimental quartermaster caught fire; the building was destroyed, but both officers escaped unharmed.

[13] In June 1891, McGunnegle received promotion to captain[5] and was assigned to command the 15th Regiment's Company I at Fort Sheridan, Illinois.

[15] During the Spanish–American War in 1898, McGunnegle was on leave visiting family in Annapolis when the 15th Infantry traveled to Huntsville, Alabama for organization and training prior to departing for combat in Cuba.

[16] McGunnegle anticipated joining the regiment in Huntsville, but subsequently received orders to perform duty as mustering officer for members of the District of Columbia National Guard who were being discharged after completing their terms of federal service.

[17] In late 1898 and early 1899, McGunnegle served as mustering out officer in Georgia and South Carolina for soldiers who were being discharged from active duty.

[18][19] In mid-1899, he was assigned to recruiting duty in Baltimore, with responsibility for enlisting soldiers to fill temporary units created for service in the Philippine–American War.

[21] In 1903, McGunnegle was assigned to the 17th Infantry Regiment and performed temporary duty as inspector of the Washington National Guard, then served again in the Philippines.

[30] Because the United States had entered World War I the previous year, McGunnegle remained on active duty and continued to command Fort McDowell.