The agreement between the airline and Expotel, the travel management firm for the Scottish Government and other bodies, will come into effect next month.
The deal, which is for business travel, will cover staff employed by organisations such as the NHS, the police force and local government, as well as MSPs.
Carolyn McCall, chief executive of easyJet, said: "We believe this new deal will not only offer public-sector workers across Scotland easy and affordable travel but will also safeguard the taxpayers' purse."
Deputy First Minister Nicola Sturgeon said: "We are always looking for ways to cut down on necessary expenses such as travel."
However, Green MSP Alison Johnstone said: "This announcement sends the worst possible signal at a time when a lot of effort is being made to get business travellers to switch to low-carbon travel to London."