Abstract. We perform a fault-based probabilistic seismic hazard assessment (PSHA) exercise in the Upper Rhine Graben to quantify the relative influence of fault parameters on the hazard at the Fessenheim nuclear power plant site. Specifically, we show that the potentially active faults described in the companion paper (Jomard et al., 2017, hereafter Part 1) are the dominant factor in hazard estimates at the low annual probability of exceedance relevant for the safety assessment of nuclear installations. Geological information documenting the activity of the faults in this region, however, remains sparse, controversial and affected by a high degree of uncertainty. A logic tree approach is thus implemented to explore the epistemic uncertainty and quantify its impact on the seismic hazard estimates. Disaggregation of the peak ground acceleration (PGA) hazard at a 10 000-year return period shows that the Rhine River fault is the main seismic source controlling the hazard level at the site. Sensitivity tests show that the uncertainty on the slip rate of the Rhine River fault is the dominant factor controlling the variability of the seismic hazard level, greater than the epistemic uncertainty due to ground motion prediction equations (GMPEs). Uncertainty on slip rate estimates from 0.04 to 0.1 mm yr⁻¹ results in a 40 to 50 % increase in hazard levels at the 10 000-year target return period. Reducing epistemic uncertainty in future fault-based PSHA studies at this site will thus require (1) performing in-depth field studies to better characterize the seismic potential of the Rhine River fault; (2) complementing GMPEs with more physics-based modelling approaches to better account for the near-field effects of ground motion and (3) improving the modelling of the background seismicity. Indeed, in this exercise, we assume that background earthquakes can only host M  <  6. 0 earthquakes. However, this assumption is debatable, since faults that can host M  >  6. 0 earthquakes have been recently identified at depth within the Upper Rhine Graben (see Part 1) but are not accounted for in this exercise since their potential activity has not yet been described.