In the fall of 1945, Convair found it was competing with itself when the USAAF became interested in an unorthodox forward-swept wing jet attack design, the XA-44-CO that the company had also been working on.

With the end of World War II severely curtailing budgets, the company considered canceling the XB-46 in favor of the other project as there was insufficient funding for both.

Company officials argued that it made more sense to allow them to complete the XB-46 prototype as a stripped-down testbed omitting armament and other equipment and for the AAF to allow them to proceed with two XA-44 airframes in lieu of the other two XB-46s on contract.

Production versions were to be equipped with a pair of .50 caliber Browning M2 machine guns in a tail turret designed by Emerson Electric Company and provision was made for an APG-27 remote control optics and sighting system, but no weaponry was fitted into the prototype.

Likewise, production aircraft were intended to be built with the General Electric J47 engines with 5,200 lbf (23 kN) static thrust rather than the J35s used on the prototype.

The XB-46's first flight occurred 2 April 1947 after a month of taxi testing, and lasted ninety minutes as the bomber departed the Convair plant in San Diego, California for Muroc Army Airfield in the high desert.

After 44 additional flight hours, the XB-46 was taken out of service, since the cost of support and maintenance, coupled with a lack of spare parts, had become prohibitive.

After sitting idle for a year, it was flown to Eglin Air Force Base, Florida, in July 1950, where its pneumatic system was tested under the coldest conditions in the large climatic facility there.