‘Sigma-movement’ is an illusory motion caused by pursuit eye movements. Three experiments examined the perceived velocity of sigma-movement by using the method of magnitude estimation. Stimuli were checkerboard patterns presented stroboscopically. In Experiment 1, we examined the effect of direction of pursuit eye movement on the perceived velocity, and found that vertical movement was perceived faster than horizontal one (anisotropy of velocity perception). In Experiment 2, we examined the effect of luminance and color (equiluminance), and found that the perceived velocity for the color stimulus was almost equal to that for the luminance stimulus. In Experiment 3, we examined the effect of stimulus size, and found that the perceived velocity increased as the size decreased. The results of Experiments 2 and 3 also confirmed the anisotropy found in Experiment 1. We discussed that the anisotropy of velocity perception of the sigma-movement is caused in the eye–head system of velocity perception.