In February 2019, a major flooding event occurred in Townsville, North Queensland, Australia. Here we present a prediction of the occurrence of mosquito-borne diseases (MBDs) after the flooding. We used a mathematical modelling approach based on mosquito population abundance, survival, and size as well as current infectiousness to predict the changes in the occurrences of MBDs due to flooding in the study area. Based on 2019 year-to-date number of notifiable MBDs, we predicted an increase in number of cases, with a peak at 104 by one-half month after the flood receded. The findings in this study indicate that Townsville may see an upsurge in the cases of MBDs in the coming days. However, the burden of diseases will go down again if the mosquito control program being implemented by the City Council continues. As our predictions focus on the near future, longer term effects of flooding on the occurrence of mosquito-borne diseases need to be studied further.