We report a theoretical investigation and elucidation of the X-ray absorption spectra of neutral benzene and of the benzene cation. The generation of the cation by multiphoton ultraviolet (UV) ionization and the measurement of the carbon K-edge spectra of both species using a table-top high-harmonic generation source are described in the companion experimental paper [Epshtein, M.; et al. J. Phys. Chem. A http: //dx.doi.org /10.1021/acs.jpca.0c08736]. We show that the ls(C) -> pi transition serves as a sensitive signature of the transient cation formation, as it occurs outside of the spectral window of the parent neutral species. Moreover, the presence of the unpaired (spectator) electron in the pi-subshell of the cation and the high symmetry of the system result in significant differences relative to neutral benzene in the spectral features associated with the ls(C) -> pi* transitions. High-level calculations using equation-of-motion coupled-cluster theory provide the interpretation of the experimental spectra and insight into the electronic structure of benzene and its cation. The prominent split structure of the ls(C) -> pi* band of the cation is attributed to the interplay between the coupling of the core -> pi* excitation with the unpaired electron in the pi-subshell and the Jahn-Teller distortion. The calculations attribute most of the splitting (similar to 1-1.2 eV) to the spin coupling, which is visible already at the Franck-Condon structure, and we estimate the additional splitting due to structural relaxation to be around similar to 0.1-0.2 eV. These results suggest that X-ray absorption with increased resolution might be able to disentangle electronic and structural aspects of the Jahn-Teller effect in the benzene cation.