When tracking visible or occluded moving targets, several frontal regions including the frontal eye fields (FEF), dorsal-lateral prefrontal cortex (DLPFC), and anterior cingulate cortex (ACC) are involved in smooth pursuit eye movements (SPEM). To investigate how these areas play different roles in predicting future locations of moving targets, 12 healthy college students participated in a smooth pursuit task of visual and occluded targets. Their eye movements and brain responses measured by event-related functional MRI were simultaneously recorded. Our results show that different visual cues resulted in time discrepancies between physical and estimated pursuit time only when the moving dot was occluded. Visible phase velocity gain was higher that that of occlusion phase. We found bilateral FEF association with eye-movement whether moving targets are visible or occluded. However, the DLPFC and ACC showed increased activity when tracking and predicting locations of occluded moving targets, and were suppressed during smooth pursuit of visible targets. When visual cues were increasingly available, less activation in the DLPFC and the ACC was observed. In addition, there was a significant hemisphere effect in DLPFC, where right DLPFC showed significantly increased responses over left when pursuing occluded moving targets. Correlation results revealed that DLPFC, the right DLPFC in particular, communicates more with FEF during tracking of occluded moving targets (from memory). The ACC modulates FEF more during tracking of visible targets (likely related to visual attention). Our results suggest that DLPFC and ACC modulate FEF and cortical networks differentially during visible and memory-guided eye tracking of moving targets.