The Scottish Government move came hours after the medicines watchdog, the Scottish Medicines Consortium (SMC), rejected ivacaftor for use on the NHS in Scotland due to cost.
It is estimated the drug would cost around £180,000 per patient for life, but would decrease as new brands entered the market.
The drug, brand name Kalydeco, treats sufferers with the G551D form of cystic fibrosis, nicknamed the Celtic mutation as it is most commonly found in Scotland and Ireland. There are around 80 sufferers in Scotland.
Without it, their life expectancy is around 34 years and they have to endure hours of physical therapy every day to clear their lungs of mucus.
It was approved for use on the health service in England on January 1 at a discount rate, but Scottish patients will have to apply on a case-by-case basis.
Campaigners welcomed the creation of the Scottish Government's £21 million Rare Conditions Medicines Fund, set aside to cover the cost of medicines whose routine use has been rejected by the SMC.
However, they warned it would leave patients competing against each other for funding.
The money will be available from March until April next year and will help cover the cost of successful requests made under the Individual Patient Treatment Request (IPTR) system, which is currently subject to a Government review.
Ed Owen, the Cystic Fibrosis Trust's chief executive, welcomed the funds but urged the drug's manufacturer Vertex, and the health service, to negotiate a fair and affordable solution to providing it routinely.
MSPs heard last year that the Individual Patient Treatment Requests (IPTR) system, which patients can use to get drugs not yet approved for general use by the SMC, is an "inequitable process" favouring young, middle-class and articulate applicants over more suitable vulnerable people who cannot speak up.
In November, Mr Neil said a review would be carried out to look at current systems for making new medicines available across the NHS.
Shadow Health Secretary Jackie Baillie MSP said: "If nothing else, it is an acceptance the current process is deeply flawed and is literally buying time while the SNP try to sort out the mess. While some Scots will benefit others won't. I hope the use of the money is reviewed regularly."
Scottish Conservative deputy leader and health spokesman Jackson Carlaw said: "This is welcome news indeed and will potentially offer hope and relief to thousands of Scots. The devil may yet be in the detail. The IPTR process has proved complicated and we need to see how accessible the new fund proves to be."
The SMC described ivacaftor as a promising new medicine but said the evidence submitted by the manufacturer was flawed.
In a statement, the SMC said: "The company's own evidence on the medicine's benefits is based on a well-designed short-term study of less than one year but the company used this study to propose an increase in life expectancy of 18 years.
"SMC considered this estimation to be highly uncertain. This weakness, combined with the very high cost of the medicine, were significant factors in the SMC decision."
Manufacturers Vertex Pharmaceuticals are expected to make a revised submission.
Health Secretary Alex Neil said: "It is only right Scottish patients with rare conditions have access to innovative medicines which are clinically justified and they are not disadvantaged due to the very high cost of these treatments.
"I am pleased to confirm the Scottish Government will establish a fund that will ensure the cost of successful new individual patient treatment requests for orphan medicines are met."
Orphan medicines are those treating illnesses affecting fewer than one in every 2000 people.