Health Secretary Shona Robison announced the scholarship at Holyrood and said she hoped it would continue the work of the 31-year-old, who died earlier this month.
After being diagnosed with the terminal degenerative disease in 2014 aged 29 while working for the Better Together campaign, Mr Aikman formed the Gordon’s Fightback campaign and raised more than £500,000 for research to find a cure.
He also successfully lobbied the First Minister to double the number of MND nurses and secured a change in the law so people at risk of losing their voice as a result of a medical condition can access voice equipment on the NHS.
Ms Robison also revealed plans for a research event on how to bring MND clinical trials to Scotland.
Scottish Labour leader Kezia Dugdale, a close friend of Mr Aikman, told parliament she would concentrate on his achievements and further work, highlighting his efforts that meant the waiting time for MND patients to be fitted with a feeding tube in NHS Lothian had dropped from 22 weeks to two weeks.