The waves and currents acting near a monopile foundation will potentially lead to scour, which may affect the stability of the wind turbine. The design of scour protection against the seabed lowering around a wind turbine monopile foundation is an important issue for wind energy industries. Many laboratory tests have been carried out to investigate the relationship between the hydrodynamic conditions and the monopile foundation scour protection layer damage, and various design criteria have been proposed. However, the experimental uncertainty of the underlying test results has not been discussed in detail. In the present research, small scale wave flume experiments of a 5m diameter monopile foundation scour protection under waves combined with currents in shallow water are described. Two groups of repetitive experiments are completed under the same wave and current conditions. The erosion development of the scour protection armor layer is measured by using a laser profiler and is evaluated based on three dimensional damage numbers. Together with visualization of the damage pattern, the damage analysis discusses the erosion in different subareas and the variances of the subarea damage number. The analysis of the uncertainty of the erosion results based on two sets of repetitive tests has been carried out. Using the uncertainty analysis methodology stated in ISO GUM standard: JCGM 100-2008, the Type A uncertainty, calibration uncertainty and combined uncertainty of the experiment are evaluated separately. The Type A uncertainty gives an overall uncertainty level and it shows that higher uncertainty occurs in the regions where stronger vortices exist. The combined uncertainty is analyzed based on scour protection dynamic stability design formula. Analysis result shows that the uncertainty due to modelling is a major source of the total uncertainty. The study gives a preliminary result of uncertainty level in wave flume test of monopile scour protection and provides a reference for future experimental research.