Billy Caldwell, who is 12, had travelled to Canada with his mother Charlotte to obtain cannabis oil after Billy's doctor was ordered to stop prescribing it.
When they flew back into London on Monday customs officials confiscated their supplies.
The boy was hospitalised on Friday after suffering several seizures.
His mother, who says Billy was free of seizures when he was using the cannabis oil, had pleaded earlier on Saturday with the Home Office, or interior ministry, to release the medication.
"Medication has been released by the Home Office and will be at hospital shortly," said a spokesman for Charlotte Caldwell in a statement to media.
The Home Office could not immediately be reached for comment. It had previously said that while it was sympathetic to his plight, it had a duty to stop banned substances from entering the UK.
Under British law, cannabis is listed as a schedule 1 drug, meaning that it is not recognised as having a therapeutic value. Schedule 1 drugs can be used for research purposes and clinical trials, but only under a Home Office licence.
The Caldwell family, who normally live in Northern Ireland, have received support from several members of parliament from different political parties.
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