Blue light absorbing flavoproteins play important roles in a variety of photobiological processes. Consequently, there have been numerous investigations of their excited state structure and dynamics, in particular by time resolved vibrational spectroscopy. The isoalloxazine chromophore of the flavoprotein co-factors has been studied in detail by time resolved Raman, lending it a benchmark status for mode assignments in excited electronic states of large molecules. However, detailed comparisons of calculated and measured spectra have proven challenging, as there are many more modes calculated than are observed, and the role of resonance enhancement is difficult to characterise in excited electronic states. Here we employ a recently developed approach due to Elles and co-workers. (J. Phys. Chem. A 2018, 122, 8308–8319) for the calculation of resonance enhanced Raman spectra of excited states, and apply it to the lowest singlet and triplet excited states of the isoalloxazine chromophore. There is generally good agreement between calculated and observed enhancements, which allows assignment of vibrational bands of the flavoprotein co-factors to be refined. However, some prominently enhanced bands are found to be absent from the calculations, suggesting the need for further development of the theory.