The trial begins on April 23 in the western German city of Koblenz, and is expected to run at least until August.
Anwar Raslan, 57, is charged with crimes against humanity, rape and 58 counts of murder, while 43-year-old Eyad Al-Gharib is accused of having been an accomplice.
Raslan allegedly led the investigations division of "Branch 251" of the Syrian secret services, which operated a prison in the Damascus area. Prosecutors say he participated in the torture and abuse of prisoners between April 2011 and September 2012.
In a statement Tuesday, the court cited the charge sheet, which alleged that around 4,000 prisoners were "beaten, kicked and subjected to electric shocks" under Raslan's leadership at the Branch 251 prison.