According to Pentagon press secretary Peter Cook, the incident took place on Tuesday while the plane was taking off.
He added that the pilot was able to eject before the crash and is currently under medical evaluation.
The crash site has been secured and the cause of the crash is under investigation, he noted.
The jet was part of the 455th Air Expeditionary Wing of the US Air Force.
F-16 fighter jets have been deployed in Afghanistan since the beginning of the US-led military in 2001. The US Air Force has maintained one squadron of F-16s at Bagram since the 2014 Washington's partial military drawdown.
Afghanistan is gripped by insecurity for around 15 years after the United States and its allies attacked the country as part of Washington's so-called war on terror.
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