The most commonly used theoretical models for describing chemical kinetics are accurate in two limits. When relaxation is fast with respect to reaction time scales, thermal transition state theory (TST) is the theoretical tool of choice. In the limit of slow relaxation, an energy resolved description like RRKM theory is more appropriate. For intermediate relaxation regimes, where much of the chemistry in nature occurs, theoretical approaches are somewhat less well established. However, in recent years master equation approaches have been successfully used to analyze and predict nonequilibrium chemical kinetics across a range of intermediate relaxation regimes spanning atmospheric, combustion, and (very recently) solution phase organic chemistry. In this article, we describe a Master Equation Solver for Multi-Energy Well Reactions (MESMER), a user-friendly, object-oriented, open-source code designed to facilitate kinetic simulations over multi-well molecular energy topologies where energy transfer with an external bath impacts phenomenological kinetics. MESMER offers users a range of user options specified via keywords and also includes some unique statistical mechanics approaches like contracted basis set methods and nonadiabatic RRKM theory for modeling spin-hopping. It is our hope that the design principles implemented in MESMER will facilitate its development and usage by workers across a, range of fields concerned with chemical kinetics. As accurate thermodynamics data become more widely available, electronic structure theory is increasingly reliable, and as our fundamental understanding of energy transfer improves, we envision that tools like MESMER will eventually enable routine and reliable prediction of nonequilibrium kinetics in arbitrary systems.