This lexical decision eye-tracking study investigated whether horizontal and vertical readings elicit comparable behavioral patterns and whether reading directions modulate lexical processes. Response times and eye movements were recorded during a lexical decision task with Japanese bimorphemic compound words presented vertically. The data were then analyzed together with those obtained in a horizontal lexical decision experiment of Miwa, Libben, Dijkstra, and Baayen (2014). Linear mixed-effects analyses of response times and eye movements revealed that, although response times and first fixation durations were notably shorter in horizontal reading than vertical reading, the vertical reading elicited fewer fixations. Furthermore, while compounds were recognized largely in comparable ways regardless of reading direction, several lexical processes were found to be reading-direction-dependent. Particularly, processing of the first morpheme was modulated by reading direction in a late time frame, such that a horizontal reading advantage was observed for words with a high frequency first morpheme. All in all, the two reading directions do not only differ quantitatively in processing speed, but also qualitatively in terms of underlying processing mechanisms.