Uber's global CEO Travis Kalanick and his South Korean partner have been charged with operating an illegal taxi service.
News service AFP reported the prosecutors' office as saying Kalanick and a local rental car service operator had been indicted for violating a law on passenger transport services.
Neither were detained, and it was not immediately clear whether Kalanick would visit Seoul for trial.
In South Korea, rental car service operators are banned from conducting passenger transport business using their cars. Violators face up to two years in jail or a fine of $18,150.
The Seoul city government has filed complaints with prosecutors, saying Uber's operations raised passenger safety issues and threatened the livelihood of licensed taxi drivers.
City regulators have launched a crackdown on drivers and rental cars that cooperate with Uber. A financial reward of up to one million won was offered for those who report Uber's activities.
California-based Uber is the most prominent of several smartphone apps that are shaking up the traditional taxi landscape in cities around the world.
It has already faced significant resistance from regulators in several countries, who accuse it of unfair competition and a lack of standards.
Uber has also sparked angry protests by cab drivers in France and other countries who fear it is chipping away at their client base.
It made headlines this month when an Uber driver allegedly raped a passenger in New Delhi.
Also the company apologized for raising prices as frightened people fled an armed cafe siege in the Australian city of Sydney last week.
The firm reportedly charged customers four times the regular fare to leave the area – a move that sparked outrage.