Jones graduated on June 12, 1912, 27th in a class of 95. Jones entered active duty and was commissioned as a second lieutenant in the 14th Cavalry. He performed troop duty at Fort Clark and Marfa, Texas from September 14, 1912, to December 2, 1913, when he volunteered for pilot instruction. Jones was detached to the Aeronautical Division, U.S. Signal Corps and assigned to the Signal Corps Aviation School at North Field in San Diego, California, on December 5, 1913. He was taught to fly by civilian instructor Oscar A. Brindley and assigned to the 2nd Company, 1st Aero Squadron on August 5, 1914. On August 19, he earned his rating of Junior Military Aviator (JMA) and was immediately placed on flight status. Congress expanded the air arm into the Aviation Section, U.S. Signal Corps in July 1914, and Jones remained assigned to the 1st Aero Squadron until September 23, 1915, when he returned to MIT for a post-graduate course on aeronautical engineering, the first such course ever, graduating on June 7, 1916. While at MIT, Jones served with both Milling and Captain Virginius E. Clark on the Technical Aero Advisory and Inspection Board in April and May 1916, testing aircraft and balloons at the Curtiss Aviation School in Newport News, Virginia, for possible use in Mexico. During 1915, Jones set two flight duration records: for an aviator alone with a flight time of eight hours and 53 minutes flying S.C. 31, a new Martin TT tractor airplane, on January 15, and for an aviator and two passengers with a flight time of seven hours and five minutes flying S.C. 28, a Burgess H with extra fuel tanks, on March 12, both at North Field. For these flights, Jones received the Mackay Trophy. On July 2 at San Diego, he became the first army pilot to execute a loop and stall an airplane without crashing, and on December 12, to execute a tail spin, flying S.C. 30, a Curtiss J tractor on both flights. Jones and First Lieutenant Thomas D. Milling, while on temporary duty from mid-April to late May 1915 at Brownsville, Texas, flew the first United States Army aerial reconnaissance mission under combat conditions on April 20, 1915. Using one end of the cavalry drill field at Fort Brown as a landing strip, the pair flew S.C. 31 to observe for movements of Pancho Villa, with Jones piloting and Milling to record the location of Villa's troops.