This paper aims to fill the gap in multi-axial fatigue characterization of concrete by presenting a comprehensive numerical analysis of data from the punch-through shear test (PTST), which allows control over combined shear and compression loads in the tested ligament. To accurately reproduce the degradation process in this multi-axial configuration, a material model must capture two key effects: (i) dissipative behavior at the inter-aggregate level during subcritical pulsating loading and (ii) fatigue-induced tri-axial stress redistribution in the test ligament. The recently published MS1 model by the authors effectively incorporates these features, thereby enabling a deeper interpretation of the experimental data. The former effect is seamlessly integrated into the model using the Lemaitre-type fatigue hypothesis, facilitating the direct derivation of general evolution equations. The latter effect is efficiently represented through the microplane homogenization framework. The model’s predictions for PTST response under monotonic shear loading with varying levels of radial confinement align well with experimental results. Similarly, the simulated fatigue response accurately reproduces the experimentally observed S-N (Wöhler) curves. Further studies demonstrate the model’s ability to predict the effect of fatigue loading sequence. A thermodynamically-based formulation provides an energetic interpretation of this effect, offering a quantitative breakdown of energy dissipation attributed to individual dissipative mechanisms over the lifetime of the material. The studies show that damage-induced dissipation remains almost constant regardless of different fatigue loading histories.