Zebra rock, found in the eastern Kimberley region of northern Western Australia, is a Late Proterozoic sedimentary rock with a rhythmic Liesegang-type Fe-oxide banding. The striped rhythmic pattern in sedimentary rocks is an important key to infer chemical conditions of water-rock reactions. Although past studies have discussed the zebra rock formation for decades, the process remains unclear. Here, we introduce a new formation model, suggesting that zebra rock formed in an acidic hydrothermal system and that pH buffering of Fe2+-bearing acidic fluid, in a neutralization reaction with primary carbonate minerals, induced rhythmic Fe-precipitation. The Fe profile clearly shows a reaction front, indicating unidirectional diffusive fluid migration along bedding planes. The two types of zebra rock distinguished by color and by clay mineral assemblages correspond with typical acidic hydrothermal alteration zonation. Although a specific volcanic event related to the hydrothermal activity cannot be identified presently, this study provides a new model for the zebra rock, recording both hydrothermal alteration and post-Late Proterozoic fluid migration.