Russian Railways is seeking two million rubles ($66,000) in damages from Apple for breach of copyright.
Russian Railways registered the suit with the Moscow Arbitration Court on Monday, but a date for a hearing has not yet been set, Vedomosti reported Tuesday.
Russian Railways, the state-owned monopoly that controls most of the nations track and rolling stock, said in a statement that Apple violated its exclusive rights to use a trademark.
At issue is an iPhone app available via Apple's App Store called RZhD Tariff.
The app, which tells users how much Russian Railways will charge for moving various cargoes from one destination to another, uses the company's distinctive red logo as part of its icon.
Proving Apple's liability for design of the applications, which are often written by independent developers, could be tricky.
A previous attempt by Cartier to hold the American technology giant accountable for a similar use of its logo in an app in 2009 failed.
According to its page on the iTunes website, the copyright for RZhD Tariff is held by its developer, Alexei Sirotkin.
It is unclear how many iPhone-wielding hipsters need to know the rate for moving 60 tons of mineral ore from Berezniki to Ufa. But if you're interested, the app was listed as available for 199 rubles on the iTunes website on Tuesday evening.
It is not the first time Apple has fallen foul of the rail sector. Last September, Swiss Federal Railways accused Apple of copying their iconic 1944-designed clock face for its new iOS6 operating system.