A VTA spokeswoman said the man disregarded the warning lights, bells and traffic gate at Southwest Expressway and South Bascom Avenue and was walking across the tracks around 10:45 a.m. when an eastbound train hit him.
The train on the Winchester-Mountain View line was approaching the Bascom station at a speed between 35 mph and 45 mph.
Investigators from the Santa Clara County sheriff's office interviewed about 20 passengers who were on the train. No injuries were reported among passengers.
The train operator is being tested for drugs and alcohol, which is standard procedure in VTA collisions.
A bus bridge between Winchester and Fruitdale stations will be in effect until about 2 p.m.