SBU drones preliminarily struck technical buildings at the facility.
The attack was the second on Vtorovo in the past month, following a previous strike on June 10.
The station is part of Transneft-Verkhnyaya Volga and serves as a key logistics hub for transporting refined petroleum products to export ports and domestic consumers.
Diesel fuel is pumped through the facility into the Moscow Ring Petroleum Products Pipeline and then delivered to major fuel depots around the Russian capital, the SBU said.
The station also supplies petroleum products for export through Baltic Sea ports, according to the agency.
SBU Alfa special forces carried out the strike as part of a 40-day operation targeting Russia approved by President Volodymyr Zelenskyy, the agency said.
SBU drones previously struck the Vtorovo facility on June 10. The agency also reported a strike on the station on May 24, which caused a large fire.