Battery energy storage system (BESS) has already been studied to deal with uncertain parameters of the electrical systems such as loads and renewable energies. However, the BESS have not been properly studied under unbalanced operation of power grids. This paper aims to study the modelling and operation of BESS under unbalanced-uncertain conditions in the power grids. The proposed model manages the BESS to optimize energy cost, deal with load uncertainties, and settle the unbalanced loading at the same time. The three-phase unbalanced-uncertain loads are modelled and the BESSs are utilized to produce separate charging/discharging pattern on each phase to remove the unbalanced condition. The IEEE 69-bus grid is considered as case study. The load uncertainty is developed by Gaussian probability function and the stochastic programming is adopted to tackle the uncertainties. The model is formulated as mixed-integer linear programming and solved by GAMS/CPLEX. The results demonstrate that the model is able to deal with the unbalanced-uncertain conditions at the same time. The model also minimizes the operation cost and satisfies all security constraints of power grid.