"For the use of the clock face on certain Apple devices such as iPads and iPhones, the parties have negotiated an arrangement that enables Apple to use the SBB station clock under a licence agreement," SBB said in a statement on its website.
The clock face which features a short second hand with a red ball at the end dates from 1944 and is still used in SBB's stations.
Both parties had agreed that the amount of the licensing fee and any further details about the arrangement "will remain confidential", the statement continued.
SBB contacted Apple in September after realizing that the new clock application included with the latest iPad operating system, iOS 6, apparently reproduced the SBB clock design.
At the time, the train operator said it was proud that the station clock face had been chosen "for 80 million iPads."