The apex court's ruling paved the way for Arroyo, 69, to walk out of the Veterans Memorial Medical Centre, where she was detained since October 2012, Xinhua news agency reported.
Theodore Te, a spokesman for the court, told a news conference that the Supreme Court, voting 11-4, annulled the criminal case against Arroyo for "insufficiency of evidence".
He said the court also ordered the "immediate release of the detained" former president.
Arroyo is currently a member of the Philippine House of Representatives having won the May elections for another term.
The Ombudsman filed the plunder case against Arroyo and nine other former government officials who allegedly misused some 366 million pesos ($7 million) lottery funds of the state-run Philippine Charity Sweepstakes Office from 2007 to 2010.
Arroyo is the second Philippine president to be jailed for plunder.
In 2001, ousted President Joseph Estrada was also jailed after an anti-graft court convicted and sentenced him to life in prison in 2007. Estrada was later freed after Arroyo pardoned him.
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