The company agreed in October to pay the lump sum so it could continue using SBB's Swiss-designed station clock face on its iPads and iPhones, the Tages-Anzeiger daily reported on its website, quoting several unnamed sources.
When contacted by AFP, SBB refused on Saturday to confirm the report.
The rail operator's spokeswoman Patricia Claivaz however told AFP in September SBB was preparing to meet with Apple to discuss why the company had begun using the famous clock on one of its new applications for iOS 6 without authorization.
She said at the time that SBB was more interested in bringing clarity to where and how Apple could use the logo than in raking in cash.
"We're rather proud that a brand as important as Apple is using our design," she said in September.
The clock was designed in 1944 by Swiss engineer Hans Hilfiker and remains the property of SBB. It is still used in SBB's stations.