British Transport Police, Metropolitan Police and the London Ambulance Service attended the incident, but the man was pronounced dead at the scene. He has not yet been named.
A British Transport Police spokesman told City A.M: “We are currently in attendance at Walthamstow Central station following a report of a person struck by a train shortly before 8.30am.
“Officers are now working to identify the person and inform his family.
“The incident is not believed to be suspicious at this stage.”
A London Ambulance Service spokesman added: “We were called at 8.24am today (18/9/15) to reports of an incident at Walthamstow Central Station, E17. We sent a number of resources to the scene including an ambulance crew, incident response officer and hazardous area response team.
The incident has caused severe delays on London Overground services between Cheshunt, Enfield Town, Chingford and Liverpool Street.
The latest update said delays of up to half an hour would continue into Friday afternoon, although the line had reopened.