The Thomas Jefferson Prize in Natural Philosophy is awarded at William & Mary's Charter Day. The faculty presents the award to a deserving undergraduate student. The prize has been endowed by the trustees of the Thomas Jefferson Memorial Foundation of Charlottesville, Virginia. The prize recognizes excellence in the sciences and honors the relationship that Mr. Jefferson enjoyed with Professor William Small, his College tutor in mathematics and natural sciences.
| 1998 | Jennifer M. Johnson |
| 1999 | Tesla E. Jeltema |
| 2000 | Ian J. Swanson |
| 2001 | Kenneth J. Davis |
| 2002 | Hanley S. Chiang |
| 2003 | James F. Cahoon |
| 2004 | Vijay R. Dondeti |
| 2005 | Megan E. Dellinger |
| 2006 | Paul A. Smith |
| 2007 | Kendra L. Letchworth |
| 2008 | Ashwin Rastogi |
| 2009 | Kelly K. Hallinger |
| 2010 | Lauren E. Miller |
| 2011 | Harry Gao |
| 2012 | Ari Cukierman |
| 2013 | Brian A. Rabe |
| 2014 | Stephen Cameron |
| 2015 | Will Bergan |
| 2016 | Isaac Alty (co-recipient) |
| 2016 | Andrew Halleran (co-recipient) |
| 2017 | Ben Zhang |
| 2018 | Likhitha Kolla |
| 2019 | Jacopo Gliozzi |
| 2020 | Grace Solini |