Ntaganda faced life in prison for a litany of crimes including directing massacres of civilians in Democratic Republic of Congo's volatile, mineral-rich Ituri region in 2002 and 2003.
Judge Robert Fremr told Mr Ntaganda that there were no mitigating circumstances, but ruled against a life sentence despite the seriousness of the charges.
Human Rights Watch welcomed the prison term.
The sentence is the longest the ICC has handed down.
Residents of the town of Kibumba walk on May 8, 2012, on the road to Rutshsuru, some 30 kilometres from the eastern Democratic Republic of Congo city of Goma, heading to the Nord-Kivu capital.
In 2013 Ntaganda became the first ever suspect to surrender to the court, after walking into the United States embassy in the Rwandan capital Kigali.
Aid groups have called the conflicts in Congo the world's deadliest since World War II.
Condemning Rwandan-born Ntaganda's "multiplicity of crimes", the judge said that "murder was committed on a large scale".
Ntaganda testified for weeks in his own defense, saying he wanted to put the record straight about his reputation as a ruthless military leader.
Prosecutors had said Ntaganda was key in planning and running operations for the Union of Congolese Patriots (UCP) rebels and its military wing, the Patriotic Forces for the Liberation of Congo (FPLC).More news: Half a million people evacuated as cyclone approaches Bangladesh and eastern India
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Ntaganda further received 28 years for the "systematic" rape of "women, girls and men" including girls aged nine and 11; a sentence 14 years for the sex slavery of child soldiers recruited by his group; and 12 years for the sexual enslavement of civilian children. These sentences ranged from eight years to 30 years of imprisonment.
The defense and prosecution has 30 days to appeal.
The six years Ntaganda has already served in custody will be deducted from his sentence, the ICC said.
He however added that Ntaganda had personally murdered a Catholic priest, setting an example for his soldiers to follow.
Placide Nzilamba, a Congolese human rights activist, said that the DRC needed proper local courts, investigators and a justice system.
"This sentence will help heal not only survivors but those who lost their loved ones during the atrocities of Bosco Ntaganda", Macky said. The court said in a statement that "issues related to the procedure for victims' reparations will be addressed in due course".
An ICC spokesman confirmed it was the heaviest ever sentence handed down to date by the court, which was set up in 2002 to try the world's worst crimes.
President Donald Trump's former national security adviser, John Bolton, past year said the USA wouldn't cooperate with the court, adding that "for all intents and purposes, the ICC is already dead to us".