The freight train derailed near Eola Road between the Aurora and Route 59 stations before 7:30 a.m.
A few inbound trains were halted while crews moved the freight train aside. Metra sent out an extra train to accommodate passengers and other trains made extra stops.
BNSF trains were moving again by 8 a.m.
Metra officials said riders should listen for platform announcements or track real-time updates on metrarail.com.