The new system will come into force from May and for the first time will give special focus to those rare conditions faced by fewer than 100 sufferers.
Health Secretary Alex Neil said yesterday: "This is a major step that will revolutionise access to new medicines and make the system better for patients.
"I believe it will lead to Scotland having a world-leading process."
A new system to replace the Individual Patient Treatment Request system - used by patients to try to access drugs not yet approved by the Scottish Medical Consortium (SMC) - will also be brought in from May, with the Peer Approved Clinical System (Pacs) aiming to give doctors more say in these decisions.
A review chaired by Professor David Webb of Edinburgh University for the SMC said the changes would "deliver substantially improved access to medicines" for those with rare and end-of- life conditions.
The new system of Pacs meetings would help provide "clarity on the clinicians' and patients' view on the need for the medicine" when decisions were being made, the review stated.
The changes are being made after the SMC was ordered to look at how it could increase flexibility when considering what drugs could be prescribed to people with rare conditions or terminal diseases.
Professor Angela Timoney, SMC chairwoman, said: "These changes will mean that patients in need of end-of-life care or who have very rare conditions will be able to access more new medicines.
"We will actively engage with patient interest groups and clinicians to put these changes into practice and work with stakeholders to put resources in place to introduce these new changes as quickly as possible.
"These medicines have previously not been viewed as cost-effective by conventional measures and we have worked hard to find a way to enable access in Scotland. We look forward to putting our proposals in place."
Andrew Powrie-Smith, director of the Association of the British Pharmaceutical Industry in Scotland, said: "We welcome the Scottish Government's intent to ensure that patients in Scotland living with rare diseases or life-limiting illness get access to the new, innovative treatments they need.
"SMC has taken a collaborative approach to developing proposals and as an industry, we look forward to continuing to work with SMC, NHS Scotland and the Scottish Government to ensure patients see a real difference in the speed and availability of the treatments they need."
James Jopling, the Scottish director for the health charity Breakthrough Breast Cancer, said the changes could result in more drugs being made available to patients "in their time of need".
He said: "Breakthrough Breast Cancer welcomes the enhanced role that patients and patients groups will now have in SMC decisions.
"By giving more weight to the value and benefit offered to patients by new medicines, we believe more drugs will be made available to those in their time of need. Last year, two very clinically effective medicines for secondary breast cancer were rejected for use on the grounds of cost, despite being highly valued by patients.
"These medicines would have given women precious additional quality time with their families and loved ones. We hope that the new system will allow drugs like these to be approved."
Scottish Labour leader Johann Lamont said: "This is a major victory for the brave campaigners who made Scotland aware of the injustices in this system for accessing rare and expensive drugs.
"Some strong voices who argued for this change are no longer with us, but I hope families will take comfort in the knowledge their campaigning efforts have brought this about."