Lindsay Sandiford was sentenced in 2013 after she was found with 4.8 kg (10.6 lb) of cocaine, estimated to be worth more than $2 million, hidden in the lining of her suitcase when she arrived on the holiday island of Bali from Bangkok.
A second British national who was serving a life sentence for drug offences, Shahab Shahabadi, was repatriated with Sandiford.
The plane taking them to London left Bali at around 12:30 a.m. on Friday, said I Nyoman Gede Surya Mataram, an Indonesian government official.
Last month, Yusril Ihza Mahendra, a senior Indonesian minister for legal affairs, said the two countries had agreed to repatriate Sandiford as she was old and unwell, and she would complete her sentence in Britain.
At a press conference in Bali's Kerobokan prison hours before the repatriation flight departed, Britain's deputy ambassador Matthew Downing said Sandiford would be "governed by the law and procedures of the UK", but said he would not speculate about any legal processes she might face.
Sandiford attended the press conference in a wheelchair, but did not speak and covered her face with her hands.
Downing said the agreement with Jakarta is reciprocal and that the Southeast Asian country can request the return of Indonesians in Britain, though no request had been made so far.
In the past year, Indonesia has released some other foreigners on death row, including five Australians, a French man and a Filipino woman.
