This paper presents the first attempt to address the uncertainty in zone temperature prediction with stochastic optimization. The uncertain zone temperature is a process uncertainty and has not been considered in the existing stochastic optimization for building control. To fill this gap, we proposed a novel formulation of stochastic optimization to handle process uncertainty in building control. Specifically, we first examined the accuracy of a typical linear model for predicting zone temperature. We then formulated the scheduling of the building cooling system as a stochastic optimization problem over a 24-hour look-ahead period to minimize the electricity cost of the studied building cooling system. After that, we applied the proposed stochastic load scheduling (SLS) to a direct expansion (DX) cooling system that serves a medium office building. Through simulation with a detailed building energy simulation software, EnergyPlus, we evaluated the operational cost and the thermal comfort compared with a deterministic load scheduling. The operation cost of scheduling was found to vary with the level of zone temperature prediction uncertainty. The proposed SLS can mitigate the impacts of uncertain zone temperature predictions on both operational cost and thermal comfort. The evaluation results indicate that the proposed SLS works better when the uncertainty level is more significant.