Concanamycin A is primarily used in scientific research as a potent and specific inhibitor of vacuolar-type H⁺-ATPases (V-ATPases). These enzymes are responsible for acidifying intracellular compartments, and by inhibiting them, Concanamycin A helps researchers study processes such as lysosomal function, receptor-mediated endocytosis, and intracellular trafficking.

It is widely applied in cell biology and immunology to block antigen processing and presentation, especially in studies involving dendritic cells and macrophages. Due to its ability to interfere with autophagy by preventing autophagosome-lysosome fusion, it is also used in cancer research to explore the role of autophagy in tumor cell survival and death.

Additionally, Concanamycin A has shown antifungal and antiparasitic activity in experimental models, making it a tool compound in antimicrobial research. However, its toxicity limits its use to in vitro studies rather than therapeutic applications.