Recently, within the space of generalized Skyrme models, a submodel with a Bogomol'nyi-Prasad-Sommerfield (BPS) bound was identified that reproduces some bulk properties of nuclear matter already on a classical level and, as such, constitutes a promising field theory candidate for the detailed and reliable description of nuclei and hadrons. Here we extend and further develop these investigations by applying the model to the calculation of nuclear binding energies. Concretely, we calculate these binding energies by including the classical soliton energies, the excitation energies from the collective coordinate quantization of spin and isospin, the electrostatic Coulomb energies, and a small explicit isospin symmetry breaking, which accounts for the mass difference between proton and neutron. The integrability properties of the BPS Skyrme model allow, in fact, for an analytical calculation of all contributions, which may then be compared with the semi-empirical mass formula. We find that for heavier nuclei, where the model is expected to be more accurate on theoretical grounds, the resulting binding energies are already in excellent agreement with their physical values. This result provides further strong evidence for the viability of the BPS Skyrme model as a distinguished starting point and lowest-order approximation for the detailed quantitative investigation of nuclear and hadron physics.