Charlotte Caldwell tried to bring the medication into Heathrow Airport in a last-ditch effort to treat her 12-year-old son Billy, but it was removed by border officials.
On Friday night the Home Office said it was in contact with Billy's medical team and would "carefully consider what options are available" if they advise a particular type of treatment is urgently required.
He said his decision was based on advice from senior doctors who have made it clear that Caldwell, who was hospitalised overnight, faces a medical emergency.
Billy Caldwell, from Castlederg, was admitted to Chelsea and Westminster Hospital in London yesterday when his seizures intensified, according to a statement from his family.
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Ms Caldwell said she believed the confiscated treatment had been moved to the Home Office and appealed to staff there to show compassion and bring it to the hospital.
Ms Caldwell credits the oil with keeping the boy's seizures at bay, saying he was seizure-free for more than 300 days while using it.
Last Monday, Ms Caldwell tried to bring a six-month supply of the oil - to treat up to 100 seizures a day - into the United Kingdom from Toronto but the substance was confiscated by officials at Heathrow airport.
Billy Caldwell had traveled to Canada with his mother, Charlotte, to buy cannabis oil when his doctor was forbidden to prescribe him, but when his mother and son returned to London, their customs authorities seized it.
She said earlier that the denial of the medicine by British officials was "beyond cruelty".
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"He has 20 days worth of anti-epileptic seizure drugs". Speaking after the Home Secretary revealed he had granted a licence for Billy, she said: "History has been made today".
"His little body has been completely broken and his little mind", she said.
"My experience throughout this leaves me in no doubt the Home Office can no longer play a role, in fact play any role, in the administration of medication for sick children in our country".
He became the first person in the United Kingdom with a prescription for cannabis oil when it was recommended to him by a local doctor in Northern Ireland.
She said: "I strongly believe that this is the first push - from here, it's a ripple effect".
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Billy and his mother had travelled to Canada to obtain cannabis oil after the boy's doctor was ordered to stop prescribing it.