Dounreay Site Restoration Limited (DSRL), the company decommissioning the site, said it was because a number of projects were nearing completion.
All the plant jobs going are expected to be voluntary redundancies.
The Unite union said it was disappointed as it believed there was enough work to support all existing jobs at the site, near Thurso.
Off the 200 jobs, 150 are expected to be voluntary redundancies at the plant, and the other 50 are in the supply chain.
Managing director Phil Craig said: "This voluntary programme will help us ensure that we have the right balance of skills to deliver the remainder of our decommissioning programme safely and securely while protecting the environment.
"The site and local community have long planned for such reductions, with more than Â£10m invested by the Nuclear Decommissioning Authority and Dounreay in projects that are helping to create new and sustainable local jobs.
"We will work with our staff and their representatives along with our supply chain partners to ensure everyone is treated fairly and with respect throughout the process."
Built in the 1950s, Dounreay was an experimental nuclear power site.
The clean up operation is currently scheduled for completion by 2029.
About 200 jobs are expected to go at the Dounreay nuclear site in Caithness over the next year.