Since 1997 the school has offered the International Baccalaureate Program. The program can be a full-diploma choice or an option for earning certificates in specific subjects. The assessments are sent to external assessors, assuring that student work conforms to program standards. Thomas Jefferson High School also offers an honor program called MYP which is a program that prepares students for the International Baccalaureate program.
CAPP
The Construction Apprenticeship Preparation Program is an integrated 4-year program for students interested in careers and apprenticeships in the construction industry. Construction, Language Arts and Math instructors team to take students through the four-year curriculum. College credit is available to enrolled students.
Emergency Preparedness Club
Each November the Emergency Response Club sponsors a Mass Casualty Incident Drill that simulates a shallow 7.2 magnitude earthquake and simulates trapping over 35 students and staff members in 12 separate buildings.
Math Team
Thomas Jefferson "Mathletes" have been active participants in state Mu Alpha Theta math competitions and have achieved noteworthy successes. They have placed in the Top 10 in national Mu Alpha Theta conventions for the last 14 years and many students have won individual championships. The team placed 7th in the nation at the 2018 nationals in Colorado Springs and 9th in the nation at the 2019 Mu Alpha Theta Nationals in Las Vegas Thomas Jefferson has hosted the Washington state Mu Alpha Theta contest since 2005. In 2011 TJHS was recognized for its "contributions to a history of outstanding mathematics service to its community" with the Mu Alpha Theta Rubin Award.
Students are able to receive vocational training at the Puget Sound Skills Center, formerly known as Sea-Tac Occupational Skills Center.
Raiderlinks
TJ’s Raiderlinks was an interdisciplinary program that prepares students for their preferred career path and is aligned with the Washington Assessment for Student Learning and Federal Way Public Schools’ literacy goals. The program offered a curriculum that integrated technology into English, social studies, and science classes. Raiderlinks was a 1997 Computerworld Smithsonian Award for Excellence winner.
Students wishing to participate in the Running Start program have dual enrollment at either Highline Community College or Green River Community College. Students may attend classes at either college or both, and can attend classes either full-time or part-time. Students must provide their own transportation, unless they are disabled and their Individual Education Plan requires the school district to provide it.
The Thomas Jefferson Speech and Debate Team placed second in state in the Washington State IE tournament in 2018. The World Schools Debate Team took home tied for 36th place honors at the national tournament in Fort Lauderdale, Florida
Athletics
TJ, a member of the Olympic Division of the North Puget Sound League since 2016, won the WIAA Washington State Boys High School Soccer Championship 8 times. Overall, Thomas Jefferson athletic teams finished 4th for the 2008–2009 season and 3rd in 2009–2010 for the South Puget Sound League all sports trophy.