The run - the latest in a series of epic endurance challenges Dr Murray has taken on - comes as the Academy of Medical Royal Colleges and Faculties in Scotland publishes a report warning the NHS needs to do more to tackle physical inactivity.
It calls for every GP in Scotland to be trained to provide advice and suggest interventions to promote physical activity, in the way that GPs are able to provide advice on alcohol and smoking cessation.
Dr Murray, a fitness champion and adviser to the Scottish government, has previously run 2,659 miles (4,279km) from John O'Groats to the Sahara desert.
Following the Namib desert run - starting on 2 February - Dr Murray and the expedition organisers will oversee donations of medical equipment to communities in the area.
The Edinburgh GP will complete the challenge with regular running partner Donnie Campbell, a former Royal Marine and fellow ultra-running enthusiast who once ran more than 180 miles non-stop from Glasgow to Skye.
The pair will aim to run at least 50km a day, and will need to drink around 10.5 litres of water each day - a challenge Dr Murray called 'a massive science experiment'. A documentary filmmaker will follow their run.
Dr Murray said: 'Having run all over the world, I can say hands down the Namib desert is the most fantastic place we could have chosen to run. It is not just putting one foot in front of the other - but also a massive science experiment. It is up to ourselves to involve the right people and do the right training to counter the extreme terrain, temperatures, and challenges that emerge. We’ll likely be drinking about 10.5 litres of water a day.'
He said that the run aimed to promote the benefit of physical exercise, pointing out that 150 minutes of exercise could add seven years to life. But he added: 'We're not asking people to run ultra-marathons.'
The Academy of Medical Royal Colleges in Scotland report says that by the end of 2016, every person entering the care system should have their physical activity levels assessed. By the end of 2015, all medical schools in Scotland should offer training on physical activity and lifestyle change advice, the report says.