In the predict-then-optimize framework, the objective is to train a predictive model, mapping from environment features to parameters of an optimization problem, which maximizes decision quality when the optimization is subsequently solved. Recent work on decision-focused learning shows that embedding the optimization problem in the training pipeline can improve decision quality and help generalize better to unseen tasks compared to relying on an intermediate loss function for evaluating prediction quality. We study the predict-then-optimize framework in the context of sequential decision problems (formulated as MDPs) that are solved via reinforcement learning. In particular, we are given environment features and a set of trajectories from training MDPs, which we use to train a predictive model that generalizes to unseen test MDPs without trajectories. Two significant computational challenges arise in applying decision-focused learning to MDPs: (i) large state and action spaces make it infeasible for existing techniques to differentiate through MDP problems, and (ii) the high-dimensional policy space, as parameterized by a neural network, makes differentiating through a policy expensive. We resolve the first challenge by sampling provably unbiased derivatives to approximate and differentiate through optimality conditions, and the second challenge by using a low-rank approximation to the high-dimensional sample-based derivatives. We implement both Bellman-based and policy gradient-based decision-focused learning on three different MDP problems with missing parameters, and show that decision-focused learning performs better in generalization to unseen tasks.