The International Crimes Division of the High Court in Kampala will preside over the trial from Monday (today).
The probe, led by a panel of three judges, is set to last for a month.
Rules of the specialised court require a suspect to go through a pre-trial session to ascertain if a case can be built.
A former Catholic who converted to Islam, Mukulu was the leader of the Allied Democratic Forces (ADF) rebels that perpetrated terror in Uganda during the 1990s.
It was originally based in western Uganda but has expanded into the neighbouring Democratic Republic of Congo (DRC).
In one of the worst attacks, more than 80 students were killed after ADF militants attacked the Uganda’ government-owned Kichwamba Technical Institute in 1998 and burnt it down.
The ADF has also been blamed for the 2016 Beni massacre and also for an attack in North Kivu on December 7, 2017, which killed 15 United Nations peacekeepers in DRC.
The group was the alleged mastermind of the killing of various Muslim leaders between 2013 and 2015.
Mukulu was arrested in 2015 in Tanzania before being extradited to Uganda.