The incident occurred at the intersection of Yosemite Avenue and the railroad tracks between Gateway Drive and E Street just after 10:30 a.m. on Wednesday.
When officers arrived, they found the person who was pronounced dead at the scene.
Their identity has not been released.
All roads initially closed due to the incident are now reopen.
The train had blocked four major intersections in the heart of the city, causing drivers to find alternative routes.
Madera police remind people to always listen for a train horn, look for crossing arms that are down, and to make sure to look both ways before crossing the tracks.