The annual production scheduling of open pit mines determines an optimal sequence for annually extracting the mineralized material from the ground. The objective of the optimization process is usually to maximize the total Net Present Value (NPV) of the operation. Production scheduling is typically a Mixed Integer Programming (MIP) type problem containing uncertainty in the geologic input data and economic parameters involved. Major uncertainty affecting optimization is uncertainty in the mineralized materials (resource) available in the ground which constitutes an uncertain supply for mine production scheduling. A new optimization model is developed herein based on two‐stage Stochastic Integer Programming (SIP) to integrate uncertain supply to optimization; past optimization methods assume certainty in the supply from the mineral resource. As input, the SIP model utilizes a set of multiple, stochastically simulated scenarios of the mineralized materials in the ground. This set of multiple, equally probable scenarios describes the uncertainty in the mineral resource available in the ground, and allows the proposed model to generate a single optimum production schedule. The method is applied for optimizing the annual production scheduling at a gold mine in Australia and benchmarked against a traditional scheduling method using the traditional single ‘average type’ assessment of the mineral resource in the ground. In the case study presented herein, the schedule generated using the proposed SIP model resulted in approximately 10% higher NPV than the schedule derived from the traditional approach.