In this study, we examined possible differences in brain activation between smooth pursuit and optokinetic reflexive (OKR) eye movements using functional magnetic resonance imaging (fMRI). Eighteen healthy subjects performed two different eye movement paradigms. In the first paradigm, smooth pursuit eye movements were evoked by a single moving dot. In the second paradigm, optokinetic eye movements without a foveal smooth pursuit component were evoked by a moving pattern of multiple dots with a limited lifetime. As expected, the two eye movement systems show overlapping pathways, but the direct comparison of the activation patterns between the two experiments showed that the frontal eye field, MT/V5 and cerebellar area VI appear to be more activated during smooth pursuit than during optokinetic eye movements. These results showed that the smooth pursuit and optokinetic eye movement systems can be differentiated with fMRI using limited lifetime dots as an effective OKR stimulus.