He led the Allied Democratic Front (ADF) forces, which operated in the west of the country in the 90s and later pledged allegiance to al-Qaeda.
The charges against Mukulu, together with 34 others, range from launching a rebellion against the Ugandan government, several counts of terrorism, crimes against humanity, aiding and abetting terrorism, and murder.
In the 1990s and early 2000s, his ADF rebel forces conducted many attacks on villages and were responsible for a violent incident at Kichwamba Technical College in 1998, where 80 students were burnt alive.
Government military pressure forced them to flee into eastern DR Congo, where they joined up with local militia and renamed themselves ADF-NALU.
Remnants of his forces have more recently been accused of being involved in a string of murders of Muslim clerics in various parts of Uganda between 2013 and 2015, who the police said had been killed for daring to oppose his movement.
Mukulu was arrested in Tanzania in early 2015 and extradited to Uganda.
The pre-trial hearing is expected to last a month.