Abstract In the recent years a rapid increase of multirotor UAVs in the commercial market is observed resulting in a large number of motor/propeller concepts and thrust architectures. The limited availability of data for the aerodynamic performance of the motor/propeller system often leads to a non-optimal operation on multirotor UAVs design points. Since experimental investigations are both cost- and time-demanding, the accurate CFD modeling of UAV propellers is crucial and highly supportive in the early design phases of multirotor UAVs. In the current study, a CFD framework is employed for the performance investigation of a small-scale three-blade propeller on a lightweight micro quadrotor UAV, designed for indoor search and rescue operations. More specifically, two widely implemented methods for propeller modeling are examined, namely the Multiple Reference Frame (MRF) and the Sliding Mesh (SM). Several operating points are investigated, corresponding to different propeller rotating speeds (RPM) and Reynolds numbers. The accuracy of each method is evaluated by comparing the CFD results with those obtained from literature experimental data. Finally, the uncertainty of the computational methods is quantified through Richardson’s extrapolation method.