Recent archaeological surveys and excavations on the island of Atauro, East Timor, identified several rock shelters with evidence for prehistoric occupation. Well-preserved rock art was found at one of these sites, Aleti Tunu Bibi. Here we present a description of the site and rock art, including the motifs and design elements, and interpret the site within the context of East Timor and the wider Asia-Pacific region. Most of the art was painted in red (likely ochre) or, in a few circumstances, black pigment (likely charcoal). Ochre was found in Pleistocene and early Holocene layers during excavations of the site. The only observed drawing, the outline of a boat in dry black charcoal, may represent a “boat of the dead” similar to those depicted on Dongson drums in the region, one of which was found recently in East Timor. That a boat is depicted in the drawing suggests that it may have been executed sometime after 2000 b.p. The Aleti Tunu Bibi rock art fits within the description of other East Timor painted rock art and shares some attributes with other sites in East Timor. However, the Aleti Tunu Bibi rock art is also distinct from sites on the mainland, and its presence on Atauro Island supports previous hypotheses of substantial local or temporal variation, and possibly indicates a pre-Austronesian origin for this tradition on the island.