Exoplanets on eccentric orbits experience an incident stellar flux that can be markedly larger at periastron versus apoastron. This variation in instellation can lead to dramatic changes in atmospheric structure in regions of the atmosphere where the radiative and advective heating/cooling timescales are shorter than the orbital timescale. To explore this phenomenon, we develop a sophisticated one-dimensional (vertical) time-stepping atmospheric structure code, EGP+, capable of simulating the dynamic response of atmospheric thermal and chemical structure to time-dependent perturbations. Critically, EGP+ can efficiently simulate multiple orbits of a planet, thereby providing new opportunities for exoplanet modeling without the need for more computationally-expensive models. We make the simplifying assumption of cloud-free atmospheres, and apply our model to HAT-P-2b, HD~17156b, and HD~80606b, which are known to be on higher-eccentricity orbits. We find that for those planets which have Spitzer observations, our planet-to-star ratio predictions are roughly consistent with observations. However, we are unable to reproduce the observed peak offsets from periastron passage. Finally, we discuss promising pathways forward for adding new model complexity that would enable more detailed studies of clear and cloudy eccentric planets as well as worlds orbiting active host stars.