A former officer in the terror group founded by infamous war lord Joseph Kony has been sentenced to 40 years in prison, after a landmark war crimes trial in Uganda.

Thomas Kwoyelo was found guilty of multiple counts of crimes against humanity in August for acts he committed while a commander in the Lord's Resistance Army (LRA).

On Friday he was sentenced to four decades behind bars, bringing to an end the first such trial of its kind in the East African country, which has suffered from decades of violence and internal unrest.

Formed in the 1980s, the LRA led a two-decade campaign of terror across a number of African countries, which saw 100,000 people killed and 60,000 children abducted.

Kwoyelo, who was abducted by the LRA at the age of 12 and became a low-level commander, has always maintained his innocence.

He was found guilty of murder, rape, torture, pillaging, abduction and the destruction of settlements for internally displaced people.

Most of his offences occurred between 1996 and 2005 in parts of northern Uganda and South Sudan.

His legal team told the court it intends to appeal the decision.

Kwoyelo was first arrested in 2009, however the case against him faced multiple setbacks and was repeatedly delayed.

The LRA's atrocities were brought to international attention more than a decade ago by the viral Kony 2012 campaign, which sought to bring him to justice.

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

Despite this, the former altar boy and self-described prophet remains at large.

ABC/AFP