Hydrological extremes affect societies and ecosystems around the world in many ways, stressing the need to make reliable predictions using hydrological models. However, several different hydrological models can be selected to simulate extreme events. A difference in hydrological model structure results in a spread in the simulation of extreme runoff events. We investigated the impact of different model structures on the magnitude and timing of simulated extreme high- and low-flow events by combining two state-of-the-art approaches: a modular modelling framework (FUSE) and large ensemble meteorological simulations. This combination of methods created the opportunity to isolate the impact of specific hydrological process formulations at long return periods without relying on statistical models. We showed that the impact of hydrological model structure was larger for the simulation of low-flow compared to high-flow events and varied between the four evaluated climate zones. In cold and temperate climate zones, the magnitude and timing of extreme runoff events were significantly affected by different parameter sets and hydrological process formulations, such as evaporation. In the arid and tropical climate zones, the impact of hydrological model structures on extreme runoff events was smaller. This novel combination of approaches provided insights into the importance of specific hydrological process formulations in different climate zones, which can support adequate model selection for the simulation of extreme runoff events.