Metaprotella sandalensis Mayer, 1898 (Caprellidae: Amphipoda: Crustacea) and related congeners are widely distributed in the Indo-West Pacific. As a first step in elucidating the species diversity of Metaprotella from the Great Barrier Reef, a new species, Metaprotella lowryi sp. nov. collected from One Tree Island in southern Great Barrier Reef is described and figured. Metaprotella lowryi sp. nov. differs from M. sandalensis [sensu stricto] by shorter antenna 1 relative to body length and shorter antenna 1 peduncle article 3. The new species of Metaprotella is also closely related to M. solitaria Takeuchi & Lowry, 2017, reported from the Solitary Islands off the northern coast of New South Wales, but differs by the characters of the head, the propodus of gnathopod 2 and the dorsodistal projections of pereonite 3.