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To incorporate uncertainties in the operational model, we formulate a two-stage stochastic programming model for the stochastic empty container repositioning (ECR) problem. This paper proposes a separable piecewise linear learning algorithm (SPELL) to approximate the expected cost function. The core of SPELL involves learning steps that provide information for updating the expected cost function adaptively through a sequence of piecewise linear separable approximations. Moreover, SPELL can utilize the network structure of the ECR problem and does not require any information about the distribution of the uncertain parameters. For the two-stage stochastic programs, we prove the convergence of SPELL. Computational results show that SPELL performs well in terms of operating costs. 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