Interocular suppression plays an important role in the visual deficits experienced by individuals with amblyopia. Most neurophysiological and functional MRI studies of suppression in amblyopia have used dichoptic stimuli that overlap within the visual field. However, suppression of the amblyopic eye also occurs when the dichoptic stimuli do not overlap, a phenomenon we refer to as long-range suppression. We used functional MRI to test the hypothesis that long-range suppression reduces neural activity in V1, V2 and V3 in adults with amblyopia, indicative of an early, active inhibition mechanism. Five adults with amblyopia and five controls viewed monocular and dichoptic quadrant stimuli during fMRI. Three of five participants with amblyopia experienced complete perceptual suppression of the quadrants presented to their amblyopic eye under dichoptic viewing. The blood oxygen level dependant (BOLD) responses within retinotopic regions corresponding to amblyopic and fellow eye stimuli were analyzed for response magnitude, time to peak, effective connectivity and stimulus classification. Dichoptic viewing slightly reduced the BOLD response magnitude in amblyopic eye retinotopic regions in V1 and reduced the time to peak response; however, the same effects were also present in the non-dominant eye of controls. Effective connectivity was unaffected by suppression, and the results of a classification analysis did not differ significantly between the control and amblyopia groups. Overall, we did not observe a neural signature of long-range amblyopic eye suppression in V1, V2 or V3 using functional MRI in this initial study. This type of suppression may involve higher level processing areas within the brain.