Suspected Lord’s Resistance Army member Thomas Kwoyelo is pictured during a pre-trial session at the High Court in Kampala on Februay 1, 2017. [AFP]

A Ugandan court on Friday sentenced a former Lord's Resistance Army (LRA) commander to 40 years in prison after a landmark war crimes trial over his role in the group's two-decade reign of terror.

Thomas Kwoyelo was found guilty in August of multiple counts of crimes against humanity in the first such trial in the East African country.

"This court has determined the 40 years sentence on the offence of murder properly reflects on the criminality of Thomas Kwoyelo," lead judge Michael Elubu said at the International Crimes Division (ICD) of the high court in the northern city of Gulu.

The LRA was founded by former altar boy and self-styled prophet Joseph Kony in Uganda in the 1980s with the aim of establishing a regime based on the Ten Commandments.

Its rebellion against President Yoweri Museveni saw more than 100,000 people killed and 60,000 children abducted in a reign of terror that spread from Uganda to Sudan, the Democratic Republic of Congo and the Central African Republic.

Kwoyelo, who was abducted by the LRA at the age of 12 and became a low-level commander, had denied all the charges against him.

But he was found guilty of a litany of charges including murder, rape, torture, pillaging, abduction and destruction of settlements for internally displaced people.

Immediately following the sentence, his lawyer told the court they intended to appeal.

Most of Kwoyelo's offences occurred between 1996 and 2005 in his home area of Amuru in northern Uganda, and parts of South Sudan.

Delayed accountability

The civil war effectively ended in 2006 when a peace process was launched, though the LRA's founder Kony has evaded capture.

Kwoyelo was arrested in March 2009 in the DRC during a sweep by regional forces against LRA rebels who had fled from Uganda two years earlier.

He was put on trial in July 2011 before the ICD, but was freed two months later on the orders of the Supreme Court as part of broad amnesty for thousands of other fighters who had surrendered.

The prosecution appealed and Kwoyelo was put on trial again, though the case was repeatedly delayed.

Kony is wanted by the International Criminal Court (ICC) for rape, slavery, mutilation, murder and forcibly recruiting child soldiers.

In 2021, Dominic Ongwen, a Ugandan child soldier who became a top LRA commander, was sentenced by the ICC to 25 years in prison for war crimes and crimes against humanity.

"Accountability for LRA war victims has been painfully inadequate and opportunities for improvement are increasingly slim, making processes in Uganda all the more important," Human Rights Watch said in a January statement on the Kwoyelo case.

The ICD was set up in 2009 as part of efforts to implement peace agreements signed the previous year between the Ugandan government and the LRA.

It has the authority to try genocide, crimes against humanity, war crimes, terrorism, human trafficking and piracy.