No trains passed through the Thuringian state capital's main station for almost two hours on Tuesday morning.
Police began searching for explosives quickly after the call came in at around 7am, but the teams and sniffer dogs found nothing.
Officers arrested the suspect, a man of around 30, about two hours later while searching in a nearby park, the Thüringische Landeszeitung reported.
The young man admitted that he had made a phone call to the police to make the false report, a police spokesman said.
Initial checks showed that he was already known to the police for several crimes, including abusing emergency phone numbers.
Even after the alert was lifted at the main train station, service was massively disrupted, with continuing delays of up to 60 minutes lasting into the afternoon.