The £80m deal has an option to extend for a further three years.
Interserve will deliver a full range of services including mechanical and engineering maintenance, catering, cleaning, office services, grounds maintenance and civil works.
The contract starts this month.
Guy Bruce, managing director – industrial at Interserve, said: “We have over 65 years’ experience delivering large-scale, safety critical projects on a variety of nuclear sites across the country.
“The wide range of services we deliver means we fully understand the nuclear industry’s required specifications and standards and through continued innovation and intelligent thinking we aim to exceed and improve on them every day.
“This is a really exciting opportunity for Interserve because not only does it significantly expand our capabilities in the sector, it gives us a footprint on many of the UK’s nuclear sites.”
Peter May, head of commercial delivery at Magnox, said: “A single facilities management contract provides us with greater flexibility and a consistent approach to the delivery of services, as we strive for innovation and greater efficiency in all areas of our business.”
Interserve is also the sole contractor in a four-year framework agreement with Magnox to design and construct facilities to store intermediate-level waste.