The agreement covers areas including employment relations, working hours, living wage, work fulfilment, equality, union recognition and facility time for union representatives.
Speaking on behalf of Prospect, national secretary Richard Hardy said: “We are very pleased that the Scottish Government continues to lead by example on this key workplace issue.
“This is an incredibly important moment for workers across the Scottish Government. Fair work offers staff the chance for fulfilment and development in their jobs, manageable workloads, job security and equality.
“Our members already know that the Scottish Government is ahead of the game on Fair Work. This agreement reinforces that commitment and sets out a clear ambition.
“I would like to thank Derek Mackay, Cabinet Secretary for Finance, Economy and Fair Work for taking this important strand of his ministerial portfolio forward and my colleague, Joy Dunn from the PCS who drove this forward on behalf of all the civil service unions.
“This is an exemplary agreement. We look forward to other public body employers coming forward to add their name to it and extending the campaign to make Scotland a ‘Fair Work' nation," Hardy concluded.