A Police and Border Guard Board (PPA) spokesperson said the accident happened after the man, whose identity is yet to be established, stepped on a section of rail at the village of Kulli, between the Kulli and Tuulevälja crossings.
"According to the train driver, the man stepped on the track unexpectedly, and the driver was unable to do anything to prevent the accident. Unfortunately, the pedestrian died of his injuries at the scene," Marko Schmidt of the PPA's Ida-Harju department said.
Schmidt stressed the importance of paying particularly careful attention near rail lines.
"While the trains may be brightly colored, and can seem some distance away, they move both quickly and quietly. This means full attention from the public when near railways is crucial" Schmidt said.
The exact circumstances of the accident are still being clarified, the PPA says.
The accident happened a little before 5.40 p.m. Monday, with the line, the Tallinn-Aegviidu route, reopening at 7.30 p.m.
The three main companies involved in rail travel in Estonia, Eesti Raudtee, which operates railtrack in Estonia, and train companies Elron and Edelaraudtee, issued a hard-hitting rail safety video last year after a spate of incidents.
Editor: Andrew Whyte