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Four of the train's carriages overturned in the incident, which happened late Wednesday.
"The train was coming from Bamako and going to Dakar when it derailed and four carriages crashed down. We have a provisional toll of five people dead and 37 injured," national emergency services spokesman Colonel Senghane Diagne told AFP.
The accident occurred around 11pm between the towns of Bala and Goudiry, in Senegal's eastern province of Tambacounda, Diagne said.
The cause of the accident was unknown, but a source at the Goudiry gendarmerie pointed out the bad state of the railways in that part of Senegal.
The train carries people several times a week between the west African capitals of Mali and Senegal.
AFP