Horizontal and vertical vergence eye movements play a central role in binocular coordination. Neurophysiological studies suggest that cortical and subcortical regions in animals and humans are involved in horizontal vergence. However, little is known about the extent to which the neural mechanism underlying vertical vergence overlaps with that of horizontal vergence. In this study, to explore neural computation for horizontal and vertical vergence, we simultaneously recorded electrooculography (EOG) and whole-head magnetoencephalography (MEG) while presenting large-field stereograms for 29 healthy human adults. The stereograms were designed to produce vergence responses by manipulating horizontal and vertical binocular disparities. A model-based approach was used to assess neural sensitivity to horizontal and vertical disparities via MEG source estimation and the theta-band (4 Hz) coherence between brain activity and EOG vergence velocity. We found similar time-locked neural responses to horizontal and vertical disparity in cortical and cerebellar areas at around 100–250 ms after stimulus onset. In contrast, the low-frequency oscillatory neural activity associated with the execution of vertical vergence differed from that of horizontal vergence. These findings indicate that horizontal and vertical vergence involve partially shared but distinct computations in large-scale cortico-cerebellar networks.