Smooth pursuit eye movements add motion to the retinal image. To compensate, the visual system can combine estimates of pursuit velocity and retinal motion to recover motion with respect to the head. Little attention has been paid to the temporal characteristics of this compensation process. Here, we describe how the latency difference between the eye movement signal and the retinal signal can be measured for motion perception during sinusoidal pursuit. In two experiments, observers compared the peak velocity of a motion stimulus presented in pursuit and fixation intervals. Both the pursuit target and the motion stimulus moved with a sinusoidal profile. The phase and amplitude of the motion stimulus were varied systematically in different conditions, along with the amplitude of pursuit. The latency difference between the eye movement signal and the retinal signal was measured by fitting the standard linear model and a non-linear variant to the observed velocity matches. We found that the eye movement signal lagged the retinal signal by a small amount. The non-linear model fitted the velocity matches better than the linear one and this difference increased with pursuit amplitude. The results support previous claims that the visual system estimates eye movement velocity and retinal velocity in a non-linear fashion and that the latency difference between the two signals is small.