The Scottish Medicines Consortium (SMC) said the makers of fingolimod, the first tablet treatment for MS, did not show it was good value for money and the body chose not to recommend it for use on the NHS.
But now the National Institute for Health and Clinical Excellence (Nice), which rules on drugs in England and Wales, has revealed draft guidance recommending fingolimod, whose brand name is Gilenya, for prescription on the NHS for some patients with relapsing-remitting multiple sclerosis.
It raises the prospect of a north-south divide for patients, even although Scotland suffers the highest rate of MS in the world, with 10,500 people diagnosed with the condition.
Dr Belinda Weller, a neurologist at the Western General in Edinburgh who led the Scottish clinical trial of fingolimod, said: "It's going to be quite hard for our patients in Scotland who are aware that people over the Border are going to be having access to this.
"But I'm also hopeful that with that decision there will be more pressure on the regulatory body in Scotland to reconsider the decision."
Fingolimod can help reduce the number of relapses in adults with relapsing-remitting multiple sclerosis.
A spokesman for the SMC said: "Sometimes SMC has to make very difficult decisions and we are acutely aware that our decisions have an impact on patients."