Battery electric bus (BEB) is getting increasing consideration from transit agencies as a sustainable public transportation alternative. Although BEBs limited driving range and longer charging duration cause concern for bus operators, fast-charging technology is a potential remedy for extending the daily driving range of BEBs while simultaneously reducing the charging duration and battery size. However, increased queue length at the terminals for fast charging can also cause a problem in adhering to BEB schedules. In this context, a comprehensive analysis is required to plan and design the BEB system considering waiting time limitations, and finding the right trade-off between battery sizes and charging infrastructure. In this study, we developed a base optimization model, as well as its stochastic version, accounting for varying energy demand scenarios under different operating conditions. Our models determined the effects of waiting time limitations over the BEB battery sizes and charger design variables (location, size, and capacity) while minimizing the total cost of the BEB system. The sample average across all the scenarios is used to estimate the stochastic optimization model objective, which is then solved using the Lagrangian relaxation method. We implemented our model over a public bus subnetwork proposed for electrification in the city of New Delhi, India. The results suggest that considering waiting time limitations at a fast-charging station can affect the system design and will help bus operators abide by the service level agreements covering trip delay, frequency, daily mileage, and so forth, made with the transit agency.