On 17 March 2006, Lubanga became the first person arrested under a warrant issued by the ICC. His trial, for the war crime of "conscripting and enlisting children under the age of fifteen years and using them to participate actively in hostilities", began on 26 January 2009, and he was found guilty on 14 March 2012, and faced a sentence of up to 30 years. On 10 July 2012, Trial Chamber I of the International Criminal Court (ICC) sentenced Lubanga to a total period of 14 years of imprisonment, also ordering that the time from Lubanga's surrender to the ICC in 2006 until the sentencing day should be deducted from the 14-year term, which means he will spend 6 fewer years in prison.
Under Lubanga's leadership, the largely Hema UPC became one of the main actors in the Ituri conflict between the Hema and Lendu ethnic groups. It seized control of Bunia, capital of the gold-rich Ituri region, in 2002, and demanded that the Congolese government recognise Ituri as an autonomous province. Lubanga was arrested on 13 June 2002 while on a mission to Kinshasa but he was released ten weeks later in exchange for a kidnapped government minister.
Human Rights Watch has accused the UPC, under Lubanga's command, of "ethnic massacres, murder, torture, rape and mutilation, as well as the recruitment of child soldiers". Between November 2002 and June 2003, the UPC allegedly killed 800 civilians on the basis of their ethnicity in the gold mining region of Mongbwalu. Between 18 February and 3 March 2003, the UPC are reported to have destroyed 26 villages in one area, killing at least 350 people and forcing 60,000 to flee their homes. Human rights organisations claim that at one point Lubanga had 3,000 child soldiers between the ages of 8 and 15. He reportedly ordered every family in the area under his control to help the war effort by donating something: money, a cow, or a child to join his militia.
The UPC was forced out of Bunia by the Ugandan army in March 2003. Lubanga later moved to Kinshasa and registered the UPC as a political party, but was arrested on 19 March 2005 in connection with the killing of nine Bangladeshi United Nations peacekeepers in Ituri on 25 February 2005. He was initially detained in one of Kinshasa's most luxurious hotels but after a few months he was transferred to Kinshasa's central prison.
The International Criminal Court in The Hague, where Lubanga stood trial
In March 2004, the Congolese government authorised the International Criminal Court (ICC) to investigate and prosecute "crimes within the jurisdiction of the Court allegedly committed anywhere in the territory of the DRC since the entry into force of the Rome Statute, on 1 July 2002." On 10 February 2006, a Pre-Trial Chamber of the ICC found that there were reasonable grounds to believe that Lubanga bore individual criminal responsibility for the war crime of "conscripting and enlisting children under the age of fifteen years and using them to participate actively in hostilities", and issued a sealed warrant for his arrest.
On 17 March 2006, Lubanga became the first person ever arrested under an ICC arrest warrant, when the Congolese authorities arrested him and transferred him into ICC custody. He was flown to the Hague, where he has been held in the ICC detention centre since 17 March 2006. Before embarking the plane, Lubanga wept openly. As of January 2009, he is one of four people being detained by the ICC, including two rebels who fought against Lubanga in the Ituri conflict: Germain Katanga and Mathieu Ngudjolo Chui. His trial opened on 26 January 2009.
On 14 March 2012 Lubanga was found guilty of abducting boys and girls under the age of 15 and forcing them to fight in a war in the Democratic Republic of Congo in 2002 and 2003. He faced a maximum sentence of 30 years when sentenced in July 2012.
On 10 July 2012, Lubanga was sentenced for 14 years by the ICC 
The sentencing was a landmark for the first permanent international criminal court, which recently celebrated its 10th anniversary. Presiding judge Adrian Fulford said the time Lubanga had spent in the court's detention centre in The Hague would be taken into account, meaning his sentence has only 8 more years to run.
Lubanga's trial, the ICC's first, led to several controversies:
The trial was halted on 13 June 2008 when the court ruled that the Prosecutor's refusal to disclose potentially exculpatory evidence had breached Lubanga's right to a fair trial. The Prosecutor had obtained the evidence from the United Nations and other sources on the condition of confidentiality, but the judges ruled that the Prosecutor had incorrectly applied the relevant provision of the Rome Statute and, as a consequence, "the trial process has been ruptured to such a degree that it is now impossible to piece together the constituent elements of a fair trial". On 2 July 2008, the court ordered Lubanga's release, on the grounds that "a fair trial of the accused is impossible, and the entire justification for his detention has been removed", but an Appeal Chamber agreed to keep him in custody while the Prosecutor appealed. By 18 November 2008, the Prosecutor had agreed to make all the confidential information available to the court, so the Trial Chamber reversed its decision and ordered that the trial could go ahead. The Prosecutor was widely criticised for his actions, but the court was also praised for its "determination to ensure fairness to the defence".
Human rights groups have expressed their concern about the narrow scope of the charges against Lubanga, and urged the Prosecutor to add more crimes to the indictment. Several organisations wrote to the Prosecutor in 2006 arguing that "the failure to include additional charges in the case against Mr. Lubanga could undercut the credibility of the ICC in the DRC. Moreover, the narrow scope of the current charges may result in severely limiting victims’ participation in the first proceedings before the ICC. This could negatively impact on the right of victims to reparations."
Lubanga's lawyer complained that the defence team was given a smaller budget than the Prosecutor, that evidence and witness statements were slow to arrive, and that many documents were so heavily censored that they were impossible to read.