Fujimori was hospitalized at the end of last year and treated for various ailments, and had only been discharged 10 days ago.
"He is not totally stable" and still "has short periods of arrhythmia," his doctor Alejandro Aguinaga told journalists.
Fujimori, 79, arrived at the Centenario clinic, where he had previously been treated, accompanied by his son Kenji. Before entering, he raised his hand to greet journalists, according to televised images.
Fujimori's pardon has drawn heavy criticism from victims of his 1990-2000 rule as well as their relatives and human rights advocates.
But he also earned respect from many Peruvians for his ruthless and unflinching campaign to defeat leftist guerrillas during his presidency.
President Pedro Pablo Kuczynski had pledged not to pardon Fujimori, but did so just days after Kenji drained votes away from a parliamentary bid on Thursday to impeach the president on suspicion of corruption, sparking speculation the pardon was a political payback.