The train from Germany's Deutsche Bahn was arriving into Basel from Hamburg at around 5pm on Wednesday when three carriages derailed, reported Swiss media.
The train was carrying 500 passengers at the time, but no one was injured in the incident.
However the derailment damaged contact points on the line.
A number of trains were cancelled or delayed on Wednesday evening, and disruption is likely to continue on Thursday.
Swiss federal railways (SBB) announced the cancellation of several long-distance train services in and out of Basel, with alternative routes suggested.
Disruption is likely to last until Friday, it said.
In a press conference, the company said the reason for the derailment was not yet clear.