Relationship between a cell-free layer and wall shear stress (WSS) in small arterioles has been of interest in microcirculatory research. However, influence of temporal variation in the cell-free layer width on the WSS in vivo has not been fully elucidated. In this study, we tested the hypothesis that the layer variation would increase the WSS, and this effect would be enhanced by red blood cell aggregation. The cell-free layer width in arterioles (29.5โ67.1ย __ฮผ__m ID) in rat cremaster muscles were obtained with a high-speed video camera, and the layer width data were introduced into WSS estimation. Dextran 500 was administrated to elevate the aggregation level of red blood cells to those seen in normal human blood. The variation of the layer was quantified by the variability (coefficient of variation), and its effect on WSS was studied under normal and reduced flow conditions. We found that the dextran-induced red blood cell aggregation significantly elevated the variability (pย <ย 0.01) at low pseudoshear rates of 9.2ย ยฑย 0.6ย s^โ1^. The WSS estimated without taking account of the variability showed underestimation of its value than that of with consideration of the variability under all flow conditions, and this effect became more pronounced with increasing the variability. The variation of the cell-free layer should, therefore, be considered in the determination of the WSS particularly in the presence of red blood cell aggregation under reduced flow condition.