The brain regions for pursuit and saccadic eye movement processing are well known. There is, however, little knowledge about the interaction between these areas during voluntary eye movements. With 8 subjects, we investigated the dynamics of cortical areas involved in control of saccadic and smooth pursuit eye movements. We explored the connectivity between V1, hMT+, and LIP. Additionally, we explored the effects caused by shifting covert attention between pursuit and saccade targets. We modeled 15 plausible models, selecting the best one using a new group comparison approach for DCM models. Effective connectivity from V1 to hMT+ was shown to depend on whether subjects attended covertly or overtly to the targets. Comparing active tracking tasks resulted in effects in accordance with current theories of the eye movement processing system.