Fujimori, already serving a six-year sentence for corruption, is accused of
ordering kidnappings and two massacres in which 25 people were killed, including
university students and a young boy, during his tenure in the 1990s.
The court said a verdict in the case would be given on April 7, following a 15-month trial.
Fujimori has said his policies during his 10-year rule in were necessary and rescued Peru from chaos, when a bloody civil war with Maoist Shining Path fighters gripped the Andean nation.
Death squad claims
The former Peruvian leader has been accused of ordering two kidnappings and a murder that took place during the "dirty war" against the Shining Path.
On November 3, 1991, a group of armed and masked soldiers known as the "La Colina" squad burst into a party in the Lima suburb of Barrios Altos, killing 15 people, including an eight-year-old boy.
Several months later, nine university students and their professor were rounded up by the same squad, taken to a deserted area of the city and executed with shots to the back of the head.
Fujimori is also charged in relation to the the kidnapping of a Peruvian journalist working for a Spanish newspaper and a businessman, both critics of his government.
His defence team says Fujimori did not know of or approve the operations and the killings.
Fujimori fled to Tokyo in 2000 while still president amid a deepening corruption scandal and sent his resignation letter by fax from his hotel.
Japan considered Fujimori, whose parents were Japanese, to be a national and refused to extradite him.
He stayed there for the next five years before flying to Chile in 2005 where he was arrested while attempting to launch another bid for the Peruvian presidency.
Two years later he was extradited to Peru.