The pilot ejected safely from the aircraft and was undergoing a medical examination, according to the Air Force official, who spoke on condition of anonymity.
Following the accident yesterday, Obama met with the pilot at Peterson Air Force Base before heading back to Washington aboard Air Force One.
Obama expressed relief that the pilot was not injured and thanked him for his service to the country, according to reporters who were traveling with the president.
Obama used the occasion to defend his approach to the Syrian conflict, warning against allowing the United States to become drawn into a new civil war in the Middle East.
The accident occurred about six miles (nine kilometers) from Peterson Air Force Base.
The cause of the crash was under investigation, the Air Force official said.