Around 1,000 fans from the Grasshopper club were returning in a special train after watching the Zurich team play to a 1-1 draw in an away game against FC Basel when the trouble broke out, according to a report from the ATS news service.
After repeatedly pulling the emergency brake, the hooligans got out of the train after it departed from Basel at the nearby Muttenz station and descended on to the tracks at around 7,20pm, ATS reported.
The SBB had to stop running trains on the route for safety reasons, Christian Ginsig, a spokesman for the state-owned rail operator said.
Police arrived on the scene but there were no initial reports of arrests.
Two tracks were opened at the Muttenz station around 8pm but trains using them had to travel at a walking pace, Ginsig was quoted as saying.
Fans reportedly pulled on emergency brakes so hard that four carriages were disabled, SDA said.
The train incident followed skirmishes between supporters for the two teams at the Basel football stadium.
A 25-year-old man was wounded in the head, Basel police said, according to an online report from the Blick newspaper.
Also, before the Grasshopper fans left Basel, 50 mask-wearing supporters of the team confronted security forces at the St. Jakob’s train station.
Police intervened and detained several people, Blick said.
The incidents came a week after police in Bern arrested 45 people following the Swiss cup final between Zurich and Basel at the Stade de Suisse.
Supporters reportedly caused extensive damage in the capital, breaking windows and damaging an escalator.
A number of police were injured in clashes with the rowdy fans.