The whale shark Rhincodon typus is a popular focal species in the marine tourism industry. We analysed 689 encounters with at least 142 individual sharks during 2008–2010 to assess their behaviour in the presence of swimmers at Tofo Beach, Mozambique. Sharks varied in size (estimated 3.0–9.5 m total length) and the majority (74%) were males. The sharks displayed avoidance behaviours during 64.7% of encounters. Encounter duration decreased significantly, from 12 minutes 37 s with undisturbed sharks to 8 minutes 25 s when sharks expressed avoidance behaviours, indicating that interactions with tourists affected the sharks’ short-term behaviour. However, during the 2.5-year study period we found no trend in the mean encounter duration, the overall expression of avoidance behaviour or the likelihood of an individual shark exhibiting avoidance behaviours. Potential effects of tourism may be mitigated by the non-breeding status and transient behaviour of sharks at this aggregation site.