Yoon, 64, arrived at the Seoul Central District Court on Monday via the underground parking to avoid public exposure, according to South Korea's Yonhap news agency.
Prosecutors read out the indictment, after which Yoon was given the opportunity to respond to the charges.
South Korean media reported that the court could begin hearing witness testimony later in the day.
The charges stem from an escalation in December, when Yoon declared martial law amid a heated dispute over the national budget. It was short-lived but plunged South Korea into political turmoil.
Yoon justified his measure by accusing the opposition of acting against the state and being infiltrated by communists, though no evidence has been provided to support these claims.
Yoon was impeached over the move and officially removed from office by the Constitutional Court on April 4.
Military witnesses have testified that Yoon ordered soldiers to forcibly remove parliamentarians from the chamber, in an attempt to block a vote that could have invalidated the martial law declaration. Yoon has repeatedly denied the allegations in public statements.
If convicted, Yoon faces a potential life sentence. The death penalty also remains legally possible, though it has not been carried out in South Korea since the late 1990s.
