There were several cancellations and delays to local and long-distance rail as well as other public transport services following the shooting, which happened around 9pm on Tuesday.
According to police, a man killed his victim with several gun shots near platform nine of Frankfurt Hauptbahnhof.
The 27-year-old man died instantly, a police spokesman told regional media on Wednesday morning.
Police said the suspected perpetrator tried to flee the scene but was arrested by officers a few metres away.
The 54-year-old suspect was to be brought to court on Wednesday. Investigators have not yet provided any information on a possible motive.
Frankfurt's main station was temporarily closed down on Tuesday after the incident while officers gathered information.
Heavily armed police officers could be seen in the station building and at the entrances, and several police vehicles were parked around the main station.
Tracks 7 to 11 remained closed until late into the night to secure evidence.
Some shops in the station also closed.
At around 4.30 am, the operation ended and the area around the crime scene was cleared.
Rail traffic in Frankfurt appeared to be back to normal on Wednesday morning.
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