Two-photon absorption (2PA), where a pair of photons are absorbed simultaneously, is recognized as a potent bioimaging technique, which depends on the quantified 2PA probability, defined as cross-section (σ2PA). The absorbed photons either have equivalent (ω1 = ω2) or different frequencies (ω1 ≠ ω2), where the former is degenerate 2PA (D-2PA) and the latter is non-degenerate 2PA (ND-2PA). ND-2PA is of particular interest since it is a promising imaging technology with flexibility of photon frequencies and enhanced cross-sections, however, it remains a relatively unexplored area compared to D-2PA. This work utilizes time-dependent density functional theory (TD-DFT) and second-order approximate coupled-cluster with the resolution-of identity approximation (RI-CC2), for the excitation from S0 to S1, to investigate σD-2PA and σND-2PA of fluorescent protein chromophore models. Interestingly, comparison of the CAMB3LYP and RI-CC2 computations show a qualitative trend in the computed σND-2PA improvements and vertical excitation energy, ΔE. As expected, the computed values of σND-2PA are quantitatively larger than σD-2PA, where chromophores with the largest values of σD-2PA show greater potential for σND-2PA improvement. Anionic chromophores demonstrated improvements up to 14%, while substantial enhancements were observed in neutral chromophores with some achieving a 30% increase.