The former head of state walked out of her VMMC suite at 2:30 p.m. still wearing a neck brace, radio dzBB's Allan Gatus reported.
She boarded a minibus inside the VMMC compound. Arroyo's belongings were also loaded into a vehicle.
Earlier on Wednesday, the Pasay City court allowed Arroyo to post P1-million bail for her temporary liberty in her electoral sabotage case.
The court, however, denied bail for her co-accused, including former Maguindanao Governor Andal Ampatuan Jr. and former Maguindanao election supervisor Lintang Bedol.
Pasay City court sheriff Rodelio Buenviaje served at past 2 p.m. the release order for Arroyo, signed by Judge Jesus Mupas, after she posted the bail.
Buenviaje arrived before 2 p.m. but said in a radio interview that they were still waiting for the Philippine National Police's Police Security and Protection Group (PSPG) to receive the order.
"Dala ko na ang release order, we are awaiting the PSPG," Buenviaje said in an interview on dzBB radio.
On Twitter, GMA News' Bam Alegre quoted Arroyo's daughter Lourdes as saying the former leader was going to her house in La Vista, Quezon City to rest.
GMA News' Lia Mañalac-del Castillo also tweeted that Arroyo may seek alternative treatment on Thursday.
Earlier, a separate report on dzRH radio said Arroyo's house in La Vista was being readied for her return.
Opposition to Arroyo's release
Crowds had gathered outside the VMMC. They included militants opposing her imminent temporary liberty as well as supporters rejoicing over her bail.
Arroyo was placed under hospital arrest at the St. Luke's Medical Center last Nov. 18 after Mupas signed the order for her arrest on charges of electoral sabotage.
The former leader was then transferred to the VMMC in Quezon City last December.
