It happened at Teasdale Quality Food on Packers Street around 8:00 am.
Atwater police say the employee was pinned underneath a forklift and train car near a loading dock.
Firefighters and paramedics were called to the scene to extract the man out from underneath.
Officials say he suffered major injuries to his leg and was flown to a Modesto hospital. Atwater police say the man was conscious and talking while being transported.
It wasn't immediately clear what caused the forklift to overturn. Authorities and CalOSHA plan to begin an investigation.