Zia, 73, is currently on trial for corruption charges in a makeshift courtroom inside a 19th-century British-built prison where she is the only inmate and in failing health.
The former prime minister had recently complained to the court that she was losing feeling in her hand and in a leg.
In an order on Thursday, the High Court instructed that Zia be admitted to Bangabandhu Sheikh Mujib Medical University.
In response to a writ petition, the court had asked the authorities to form a fresh five-member medical board to examine Zia's health condition and start her treatment.
Zia was admitted to Bangabandhu Sheikh Mujib Medical University Saturday afternoon amid tight security, Daily Star reported.
A police car brought the Bangladesh Nationalist Party chief out of the prison. Many BNP activists were at the hospital to see Khaleda, but were blocked from approaching her by police.
Zia was jailed for five years in February after being convicted of corruption, a sentence that triggered clashes between police and thousands of her supporters.
She was granted bail in a corruption case in May but remains in jail while she fights dozens of other violence and graft charges.
Zia was found guilty then of embezzling money intended for an orphanage, a charge she dismissed as politically motivated.
She is appealing against the verdict which bars her from standing in a general election to be held in December.