We assessed the impact of a single application of wood biochar on soil chemical and physical properties and aerobic rice grain yield on an irrigated kaolinitic clay Ferralsol in a tropical Savannah. We used linear mixed models to analyse the response of soil and plant variables to application rates of biochar (0, 8, 16 and 32 t ha−1) and mineral N fertilization (0, 30, 60 and 90 kg N ha−1), and their interaction. The response was analysed within three aerobic rice-growing seasons (S), equivalent to 1.5, 2.5 and 3.5 years after biochar application (S1.5, S2.5 and S3.5). The fraction of oxidisable C in soil increased with biochar application rate, irrespective of N fertilization, at S2.5 and S3.5, whereas the rice stress-free available water (soil water retention between − 6 and − 100 kPa) decreased with biochar application rate at S1.5 and S2.5. Rice grain yield and yield components varied with the seasons according to the changes in soil properties and weather conditions. A single application rate up to 32 t ha−1 of the wood biochar type used in this study had no impact on aerobic rice yield increase on a kaolinitic clay Ferralsol under the climatic conditions of the Brazilian Savannah prone to dry spells. Most likely, the beneficial effects of wood biochar on soil chemical properties on rice production were offset by a decrease in soil water retention capacity and N uptake by the crop.