Mr Aikman was diagnosed with MND at the age of 29, and has been raising funds for research into the degenerative condition for two years.
His Gordon's Fightback campaign has won support from all of Scotland's political leaders.
He said had "never dreamed" of raising so much "life-changing" money.
The former gymnast and political campaigner has pledged to "keep on fighting" with all the energy he has left.
As Mr Aikman's condition has deteriorated, he has been restricted to a wheelchair and needs help breathing - he says he is "in a lot of pain". As it stands there is neither a cure nor an effective treatment.
But his campaign - as well as convincing the government to fund a larger team of specialist MND nurses - has won dozens of awards, including a British Empire Medal for Mr Aikman and the Public Campaigner of the Year title at the Scottish Politician of the Year Awards.
He said: "Right here in Edinburgh today there is research happening which wouldn't be happening otherwise, without this money.
"This money is going to bring forward a day when we find a cure for the thing that's killing me and far too many other people.
"It's certainly not mission accomplished - until we find a cure for motor neurone disease we all still have a job to do. And with all the energy I've got left I'm going to keep on fighting.
"This is a massive milestone, but it's not the end."
Scottish motor neurone disease campaigner Gordon Aikman has celebrated hitting his fundraising target of £500,000.