The lab’s primary mission is to conduct basic research of the atom's nucleus using the lab’s unique particle accelerator, known as the Continuous Electron Beam Accelerator Facility (CEBAF). Jefferson Lab also conducts a variety of research using its Free-Electron Laser, which is based on the same electron-accelerating technology used in CEBAF.

In addition to its science mission, the lab provides programs designed to help educate the next generation in science and technology, and to engage the public.

Managing and operating the lab for DOE is Jefferson Science Associates, LLC. JSA is a limited liability company created by Southeastern Universities Research Association and PAE Applied Technologies.