In regions with large, mature fault systems, a characteristic earthquake model may be more appropriate for modelling earthquake occurrence than extrapolating from a short history of small, instrumentally observed earthquakes using the Gutenberg–Richter scaling law. We illustrate how the geomorphology and geodesy of the Malawi Rift, a region with large seismogenic thicknesses, long fault scarps, and slow strain rates, can be used to assess hazard probability levels for large infrequent earthquakes. We estimate potential earthquake size using fault length and recurrence intervals from plate motion velocities and generate a synthetic catalogue of events. Since it is not possible to determine from the geomorphological information if a future rupture will be continuous (7.4 ≤ M W ≤ 8.3 with recurrence intervals of 1,000–4,300 years) or segmented (6.7 ≤ M W ≤ 7.7 with 300–1,900 years), we consider both alternatives separately and also produce a mixed catalogue. We carry out a probabilistic seismic hazard assessment to produce regional- and site-specific hazard estimates. At all return periods and vibration periods, inclusion of fault-derived parameters increases the predicted spectral acceleration above the level predicted from the instrumental catalogue alone, with the most significant changes being in close proximity to the fault systems and the effect being more significant at longer vibration periods. Importantly, the results indicate that standard probabilistic seismic hazard analysis (PSHA) methods using short instrumental records alone tend to underestimate the seismic hazard, especially for the most damaging, extreme magnitude events. For many developing countries in Africa and elsewhere, which are experiencing rapid economic growth and urbanisation, seismic hazard assessments incorporating characteristic earthquake models are critical.