Pascal Simbikangwa was arrested on the French island of Mayotte in 2008 and has been detained in the country since then.
At the time the killing broke out, Simbikangwa was an intelligence officer in Hutu President Juvenal Habyarimnana's government. When Habyarimnana was assassinated, violence across the country resulted in the killing of an estimated 1 million Tutsis in just a month's time.
Simbikangwa was charged with complicity in the genocide, France 24 reported.
Rwandan Justice Minister Johnston Busingye said he welcomed the landmark trial, Radio France Internationale reported.
"It is history being made. We have always wondered why it has taken 20 years. ... It is late, but it is a good sign," he said. "We will be very supportive of the process, we will cooperate."
If he's convicted, Simbikangwa could face life in prison.