In the last few decades, the Limpopo River Basin (LRB) has experienced a number of extreme rainfall events which were responsible for considerable socio-economic and environmental impacts. Most of the population here is poor and dependent on rain-fed agriculture. In order to better understand these events over the LRB, CHIRPS, 0.05° gridded rainfall data are used to identify the daily extreme events, analyse their interannual variability and examine relationships with large scale climate modes over the 1981–2016 period. Analysis of the top 20 events suggests a pattern with rainfall generally decreasing from the eastern to western parts of the basin. Typically, the highest rainfall amounts occur over the regions where there are steep topographical gradients between the mountainous regions of northeastern South Africa and the Mozambican floodplains. Almost half of the top 200 extreme events are associated with tropical extra-tropical cloud bands (48%), with tropical low-pressure systems (28%), Mesoscale Convective Systems (14%), and cut-off lows (10%) in the mid-upper atmosphere, also making sizeable contributions. The monthly distribution of the events showed that most of the events occurred during the late summer months (January–March) when tropical lows and cloud bands are more common. On interannual time-scales, most of the summers with above average number of events coincide with La Niña conditions and, to lesser extent, a positive subtropical South Indian Ocean Dipole.