In this study, the thermodynamics and barrier heights associated with the fragmentation reactions of a set of fifteen 1,4,2-oxaselenazoles into isoselenocyanates (molecules with promising anticancer activity) and carbonyl derivatives, have been studied using the high-level CBS-QB3 quantum chemical protocol. Of the systems studied, attachment of a CF3-substituent at the C5-position affords the system with the largest gas-phase free energy barrier (190.1 kJ mol–1), whilst substitution at the C5-position with two –NMe2 substituents affords a heterocycle with the lowest free energy barrier (67.8 kJ mol–1). The presence of solvent (acetonitrile) was shown to reduce the free energy barriers in all cases, with the two systems mentioned above having condensed-phase free energy barriers of 180.8 and 42.0 kJ mol–1, respectively.