Fluctuations in the profile of the ocean floor can lead to large variations in tsunami wave height. A theory linking this behaviour to the branched flow characteristics of electron waves through semiconductors may provide a framework for prediction. Tsunamis exhibit surprisingly strong height fluctuations. An in-depth understanding of the mechanisms that lead to these variations in wave height is a prerequisite for reliable tsunami forecasting. It is known, for example, that the presence of large underwater islands1 or the shape of the tsunami source2 can affect the wave heights. Here we show that the consecutive effect of even tiny fluctuations in the profile of the ocean floor (the bathymetry) can cause unexpectedly strong fluctuations in the wave height of tsunamis, with maxima several times higher than the average wave height. A novel approach combining stochastic caustic theory and shallow water wave dynamics allows us to determine the typical propagation distance at which the strongly focused waves appear. We demonstrate that owing to this mechanism the small errors present in bathymetry measurements can lead to drastic variations in predicted tsunami heights. Our results show that a precise knowledge of the ocean’s bathymetry is absolutely indispensable for reliable tsunami forecasts.