The accident happened around 2 o'clock at the restaurant along US Highway 36 on the west side of town.
Witnesses on the scene said an ambulance took the driver, 45-year-old Leavenworth resident Richard Lutgen, to the hospital for treatment.
Bob Ryser, A Wathena firefighter, said Lutgen was talking after the accident, but seemed confused and did not remember what happened. Ryser said it appeared Lutgen suffered some type of medical problem.
No one else in the restaurant was hurt, but a group of officers from Doniphan County had just left the building prior to the crash. They were there for a meeting and witnessed the accident as it happened.
Ryser said they saw the van go airborne before crashing into the Pizza Hut.
Authorities are still investigating.