The 78-year-old was being held in Kober Prison in Khartoum while he is tried alongside former ministers over the 1989 coup that brought him to power. He was removed by the army in April 2019 after months of mass protests against his rule.
His lawyer, Hashim Abu Bakr, said he had petitioned the court to transfer Al Bashir to a hospital, saying blood pressure and kidney issues posed a threat to his life if left untreated in prison.
A transfer from prison to hospital earlier this year brought controversy after images and footage emerged of him walking around a hospital ward.
In the video, Al Bashir can be seen greeting visitors outside his room, smiling and walking within the ward, dressed in casual clothing and wearing a watch.
They were the first publicly available images of Al Bashir outside of courtroom coverage since his initial arrest.
The deposed dictator is facing a litany of criminal charges. He was first jailed for corruption, receiving illegal gifts and possessing foreign currency in December 2019 and sentenced to two years in a reform facility, rather than a prison, on account of his age.
As well as his trial for the 1989 coup, he currently faces charges of corruption as well as pressure from the International Criminal Court for his extradition to face trial for war crimes relating to Darfur.