Henderson received his BS in chemistry from the University of Florida in 1992, a PhD in organic chemistry from Georgia Tech in 1999, and was an NIH Postdoctoral Fellow at MIT from 1999-2002 in the Division of Biological Engineering. His postgraduate work focused on the chemistry of DNA damage, which led him to work at Lawrence Livermore National Laboratory (LLNL) as a biomedical scientist for five years prior to his current positions.