Booster chlorination designs have been widely based on predefined (deterministic) network conditions and they perform poorly under uncertainty in water distribution systems (WDSs). This paper presents a scenario-based robust optimisation approach which was developed to obtain booster chlorination designs that withstand uncertain network operations and water demand conditions in the WDSs. An optimisation problem was formulated to minimise mass injection rates and the risk of chlorine disinfection. This problem was solved by a non-dominated sorting genetic algorithm (NSGA-II). The proposed approach was demonstrated using the Phakalane network in Botswana. The results present robust booster chlorination (RBC) designs, which indicate the number of boosters, locations and injection rates in the network. The performance of RBC designs evaluated under uncertainty reveals lower risks of chlorine disinfection compared to deterministic-based designs. The proposed approach obtains booster chlorination designs that respond better to uncertainty in the operations of WDSs.