In 2003, Schaefer received the American Chemical Society Award in Theoretical Chemistry and the Ira Remsen Award of Johns Hopkins University. In 2004, a six-day conference was convened in Gyeongju, Korea on the “Theory and Applications of Computational Chemistry: A Celebration of 1000 Papers of Professor Henry F. Schaefer III.” Schaefer was honored with the $10,000 Joseph O. Hirschfelder Prize in 2005 by the University of Wisconsin's Theoretical Chemistry Institute, joining a distinguished list of some of the best-known scientists in the field.