The decision has fumed several outrageous protests across the country as the former dictator is seen as a deeply divisive figure in Peru.
The president, who survived a motion against his regime with just one vote, said in a statement on Sunday night that he had "decided to concede a humanitarian pardon to Alberto Fujimori".
"A medical panel has determined Mr Fujimori has a progressive, degenerative and incurable disease and the jail conditions present a grave risk to his life and health," the Guardian quoted the president as saying in a statement.
The move comes a day after the former ruler was rushed to hospital on Sunday after suffering a severe drop in blood pressure and abnormal heart rhythm.
Fujimori was sentenced for 25 years after he was convicted of corruption and human rights violation charges in 2009.
Fujimori's son Kenji, who is also a Congressman, thanked the president in a tweet for his "noble and magnanimous gesture" on behalf of the Fujimori family, adding "we are eternally grateful to you".
"It's a night of joy and happiness," said Keiko Fujimori, speaking outside the hospital where her father was being treated. "It's been more than 10 years of waiting with my father without liberty. Finally justice has done, she added. (ANI)