The transport and logistics company said in a statement it was also offering customers "various alternative options of payment" for euro- and US-dollar transactions involving sanctioned lenders, including through other banks.
The West is shutting off Russia's economy from the global financial system, pushing international companies to halt sales, cut ties, and dump tens of billions of dollars' worth of investments.
It was not clear from what date FESCO began accepting payment in yuan. The company did not immediately respond to Reuters' questions.
FESCO's statement, posted on Monday, is a concrete example of how Russian companies are exploring workarounds with emerging market allies, especially China.
Chinese businesses and banks have also been scrambling for ways to limit the impact of sanctions on their relations with Russia, with settlement of transactions in yuan seen rising at the expense of the dollar.
FESCO, which operates ports, terminals and vessel fleets, said it continues to provide logistics services on all existing routes in full, adding "all settlements and payments in Russian roubles are effected as per normal."
The company works in the Russian Far East and contributes to growing trade between Russia and Asian countries, FESCO said on its website.