The employee was driving a black Toyota Camry when he or she failed to "follow directions of the gate sentry" around 7 a.m. local time, a post said.
A lockdown ensued, and authorities began searching the base for the driver and the vehicle. The vehicle was found around 9:30 a.m. CT, and the driver was located not long after.
"The driver is an employee on the base with authorized access," the post said.
Personnel were sweeping the vehicle and the area with military dogs and several buildings were evacuated. No one was injured and there was no damage to property.
An earlier post said the driver was in custody and was being questioned.
The lockdown was lifted by early afternoon and the base returned to normal operations.
A civilian vehicle also caught fire off base, but that incident was unrelated to "the gate runner," the post said.
Naval Station Great Lakes, north of Chicago on the shore of Lake Michigan, is the Navy's largest training base, according to its website.