Dr Abbas Khan, 32, was on the verge of being released when his family were told of his death.
His relatives have said he was the victim of a political murder, but the Syrian government have called his death suicide.
The orthopaedic surgeon from London was captured in November 2012 in the ancient city of Aleppo after travelling from Turkey to help victims of hospital bombings.
Nabeel Sheikh, solicitor for Dr Khan's family, issued a statement which read: "Dr Khan's family would like to thank everyone for their help and support. The family are relieved that his body has been repatriated."The Home Office is organising the process but, as a matter of course, Scotland Yard is actively involved, given the circumstances surrounding Dr Khan's death are highly suspicious.
His mother Fatima Khan disputes claims made by Syria that he killed himself.