Thunderstorms represent a major hazard for flights, as they compromise the safety of both the airframe and the passengers. To address trajectory planning under thunderstorms, three variants of the scenario-based rapidly exploring random trees (SB-RRTs) are proposed. During an iterative process, the so-called SB-RRT, the SB-RRT∗ and the Informed SB-RRT∗ find safe trajectories by meeting a user-defined safety threshold. Additionally, the last two techniques converge to solutions of minimum flight length. Through parallelization on graphical processing units the required computational times are reduced substantially to become compatible with near real-time operation. The proposed methods are tested considering a kinematic model of an aircraft flying between two waypoints at constant flight level and airspeed; the test scenario is based on a realistic weather forecast and assumed to be described by an ensemble of equally likely members. Lastly, the influence of the number of scenarios, safety margin and iterations on the results is analyzed. Results show that the SB-RRTs are able to find safe and, in two of the algorithms, close-to-optimum solutions. © 2021 The Authors