Zinc is an essential metal involved in many physiological processes. Previous work has identified a set of zinc transporters involved in Drosophila dietary zinc absorption. However, zinc excretion and reabsorption, the other two important processes to maintain zinc homeostasis, are not as well understood. In this work, we screened all the potential zinc transporter Zip (SLC39) and ZnT (SLC30) members for their likely roles in zinc excretion in Malpighian tubules, an insect organ functionally analogous to mammalian kidneys. Zip71B (CG10006, most homologous to hZIP5), in addition to the previously characterized ZnT35C (CG3994), was identified as being critical in zinc excretion. Tubule-specific knockdown of Zip71B/dZip5 reduces zinc accumulation in the tubules, but increases zinc levels in the body, resulting in survival defect under zinc excess conditions. Zip71B/dZip5 is localized to the plasma membrane at the basolateral side of the tubules, and is functionally epistatic to the apically localized ZnT35C in regulating the tubule zinc homeostasis. Our results indicate that Zip71B/dZip5 is involved in zinc import into the tubular cells from the circulation, and ZnT35C in turn effluxes the tubular zinc out. Notably, mammalian ZIP5, which is expressed in the kidney, functions analogously to Zip71B/dZip5 in the fly while hZIP4 cannot complement the loss of Zip71B/dZip5 function. Furthermore, Zip71B/dZip5 expression is regulated by zinc so that, in response to toxic levels of zinc, the tubules can increase zinc efflux capability. We also characterized the role of dZnT1 (CG17723) in zinc reabsorption in Malpighian tubules. Finally, using a tubule calcification model, we were able to show that knockdown of Zip71B/dZip5 or ZnT35C was able to mitigate stone formation, consistent with their roles in tubular zinc homeostasis. Our results start to sketch out a relatively complete picture of the zinc excretion process in Drosophila Malpighian tubules, and may provide a reference for relevant mammalian studies.