Operational decisions for crude oil scheduling activities are determined on a daily basis and have a strong impact on the overall supply chain cost. The challenge is to develop a feasible schedule at a low cost that has a high level of confidence. This paper presents a framework to support decision making in terminal-refinery systems under supply uncertainty. The proposed framework comprises a stochastic optimization model based on mixed-integer linear programming for scheduling a crude oil pipeline connecting a marine terminal to an oil refinery and a method for representing oil supply uncertainty. The scenario generation method aims at generating a minimal number of scenarios while preserving as much as possible of the uncertainty characteristics. The proposed framework was evaluated considering real-world data. The numerical results suggest the efficiency of the framework in providing resilient solutions in terms of feasibility in the face of the inherent uncertainty.