The pilot successfully ejected from the fighter, and was being treated at a local hospital, the base said in a Facebook post.
The crash occurred at about 7:16 p.m., about 80 miles southeast of Holloman, the base said. Emergency response teams were on their way to the scene Tuesday night, and a board of officers will investigate the crash, Holloman said.
It is not yet known what caused the crash.
Another F-16, from Spangdahlem Air Base in Germany, crashed in western Germany earlier this month. Its pilot also ejected, sustaining minor injuries.
And in May, an F-16 crashed into a warehouse at March Air Reserve Base in California after experiencing hydraulic problems that caused the pilot to lose control of the aircraft. That pilot safely ejected, but a dozen people on the ground were sent to hospitals for evaluation after they were exposed to debris. Miles of freeway around the area had to be closed until munitions from that jet were destroyed.