This paper presents an approach using a combination of data-driven and analytical models to design the layout of empty container depots where top-lifters (TLs) are used. A method to determine the optimum number of blocks along with the number of driving lanes is proposed where the size of the blocks is specified by the number of rows, tiers, and bays. For estimating the effects of the design variables on the TL cycle time, formulas to calculate the expected travel distance of these vehicles are derived based on geometry and a Markov chain model is used to obtain the times of retrieval and placement by the TLs using data gathered in an empirical study from a typical empty container yard. Together, the total cycle time (travel, retrieval, and placement) is then used as the objective function to evaluate alternative container yard layout options. Numerical examples from a case study are provided to illustrate the layout design procedure and show its effectiveness and pragmatism.