The Fermi National Accelerator Laboratory is a U.S. Department of Energy national laboratory site on Batavia's east side. The laboratory, called Fermilab for short, is known for having the second-highest energy proton-antiproton collider, or particle accelerator. The facility opened in 1967.

Batavia is home to the second highest number of Fermilab employees behind Aurora, according to the lab's Frequently Asked Questions web page. About 2,000 people work at Fermilab.

Fermilab is the site of several educational and recreational programs open to the public. Events are held in the 16-story Wilson Hall and Ramsey Auditorium. Other parts of the 6,800-acre Fermilab campus open to the public include programs at the Lederman Science Education Center and a dog training area on the east side of the campus.