A comparative evaluation of the fatigue damage occurring in the blades of small wind turbines, with different power regulation schemes, has been conducted for the first time. Three representative test cases were built, one based on stall regulation and two using pitch regulation. The power curves were tuned to be identical in all cases, in order to allow for a direct comparison of fatigue damage. A methodology combining a dynamic simulation of a wind turbine forced by stochastic wind speed time series, with the application of the IEC 61400-2 standard, was designed and applied for two levels of turbulence intensity. The effect of the wind regime was studied by considering Weibull-distributed wind speeds with a variety of parameter sets. Not unexpectedly, in typical wind regimes, stall regulation led to a generally higher fatigue damage than pitch regulation, for similar structural blade design, but the practical implications were smaller than thought previously. Given the need for cost-effective designs for small wind turbines, stall regulation may be a viable alternative for off-grid applications.