The first flight of the N-9M-2 took place on 24 June 1943 at Northrop Field in Hawthorne, California. Northrop test pilot John Myers was forced to land after just five minutes because the canopy was lost during takeoff. He brought the N-9M-2 in for a safe landing, but the airplane sustained minor damage to the radio mast and yaw meter, as well as a landing gear door.

On 21 September 1943, the N-9M-2 began to provide the first reliable drag data. It indicated that the full-scale XB-35 would suffer greater drag than had been predicted in wind-tunnel model tests. The N-9M-2 exhibited satisfactory longitudinal and lateral stability, but there was some difficulty with directional control.

John Myers continued to fly the N-9M until he was injured in a high-speed taxi accident in the XP-56 in September 1943. Two other Northrop test pilots, Harry Crosby and Alex Papana, were brought in to continue the program.

Sometime during October 1943, the N-9M-2 was modified with leading edge slats and Harry Crosby checked them out in a test flight on 25 October. Crosby conducted limited testing throughout the remainder of the year.

In December 1943 Northrop's chief aerodynamicist, Dr. W. F. Sears, contracted Crosby to conduct a series of test flights with two sets of auxiliary fins of different sizes, added to the top of the driveshaft housings on the N-9M-2. The purpose was to determine the effect of increased directional stability on the lateral-directional dynamic stability and drag effects.