With the expansion of the high-speed railway (HSR) network in China, high-speed rail express delivery (HSReD) is being used to satisfy the increasing demand for express cargo. The decisions on transportation resources arrangement and freight flow allocation are two of the key issues for practical implementation of HSReD. In this study, we examine the above key issues by developing a two-stage stochastic integer linear programming model to maximize the expected net operation profit of HSReD. A meta-heuristic solution approach introduced some tailored tactics is proposed to speed up the process of solving the above model in the large-scale instances. Numerical experiments based on different sizes and practical investigation on China Railway Nanchang Group are conducted to validate the effectiveness of the proposed model and solution approach. Some managerial implications are also obtained based on the sensitivity analysis, which may be potentially useful for optimizing the daily operation management of HSReD.