The charity topped an internal poll of nominations from ScotRail Alliance employees, who will raise money for the charity in a variety of events over the next three years.
It is expected that the partnership will be worth at least £150,000 over the three years.
Speaking at the Euan MacDonald Centre for Motor Neurone Disease Research, Rob Shorthouse, the ScotRail Alliance’s communications director, said: “I am absolutely delighted that we will be working with MND Scotland over the course of the next three years. I know that our 7500 staff will be doing everything they can to raise as much money as possible to help find a cure for this most terrible of diseases.
“However, it is not just about the money that we will raise while we are working together. We will also work hard to raise awareness of MND and to help support the people who are living with it.
“MND Scotland is an extraordinary charity doing extraordinary work right across our country. We are really proud that our staff and customers will have the opportunity over the next three years to help support them.”
Craig Stockton, CEO of MND Scotland, said: “We are thrilled to be named as the ScotRail Alliance’s charity partner.
“Knowing that so many ScotRail and Network Rail employees voted for MND Scotland and want to help us in the fight against Motor Neurone Disease is inspiring. Staff, customers and partners will now play a vital role in taking us closer to a cure for MND and help us support those affected in their local areas.
“This is also a fantastic opportunity for us all to raise greater awareness and help more people understand the impact of this devastating disease.
“This is a journey to find a cure and improve the lives of those affected by MND across Scotland. Through this partnership we can make a real difference.”
The ScotRail Alliance, and its 7500 employees, will be supporting the charity with a wide range of activities across the country, including dress-down days, and an RSNO concert in a ScotRail station.