German railway operator Deutsche Bahn (DB) appointed a jury that included two historians to name its fleet of new InterCityExpress trains after historical figures, and sought customers' suggestions.
Anne's name was one of 25 selected for a shortlisted.
But the move met criticism, with German MP Iris Eberl tweeting "naming a train after Anne Frank is callous".
The operator has since issued an apology, saying its intention was “in no way intended to damage the memory of Anne Frank”, adding: “Rather, the DB, conscious of its historical responsibility, decided to keep the name of Anne Frank alive.”