The 30-year-old was honoured for his services to MND awareness and research.
Since being diagnosed in 2014, his campaign – Gordons Fightback.com – has raised more than £400,000 for research into a cure for the terminal condition.
In an afternoon ceremony yesterday, the Lord Lieutenant of Edinburgh, Lord Provost Donald Wilson, presented the medal to him on behalf of the Queen.
Mr Aikman, who was diagnosed with the terminal disease at the age of 29, is now confined to a wheelchair.
The former political aide said of the accolade: “I am absolutely delighted to receive this honour.
“It might be too late for me, but we can and we must find a cure for future generations. With every day I have left I will be fighting for a world free from MND.”
Last month, Mr Aikman revealed that his campaign had reached the £400,000 mark in his bid to fund research into a cure.
The Gordon’s Fightback initiative has already secured public funding for specialist MND nurses in Scotland and won a pledge from the Scottish Government to give specialist communications equipment to patients who lose their voice as a result of the disease.
This was after it emerged that at any one time there are around 400 people living with MND in Scotland, while there were only seven specialist nurses for the whole of the country.
His outspoken comments and campaign also prompted a series of comedians to take part in fundraising gigs under the Stand up to MND banner, which contributed to ever-increasing fundraising pot for Gordon’s Fightback.
Mr Aikman was also honoured at the Politician of the Year awards as Campaigner of the Year.
During his acceptance speech, he made a plea for carers to be paid the living wage, saying: “Carers are my hands, arms and legs. They are my independence, my freedom. Carers allow me not just to live but to enjoy life.
“And with no cure for the thing that is killing me, carers do more to improve the quality of my life than any doctor ever could.”
He spoke out about the fact that a consultant could earn in six weeks what a care worker earns in one year, and added: “That can and must change”.
Earlier this year, he received an honorary degree from Edinburgh University.
He was recognised for his contribution to improving research and care for patients.
Researchers still do not know what causes MND or a cure, and half of sufferers die within 14 months of diagnosis.
Mr Aikman has spoken out about the fact that, despite this, it can take up to seven months to process applications for the benefits they need such as Personal Independence Payments.