The control of the intracellular pH is vital for the survival of all organisms. Membrane transporters, both at the plasma and intracellular membranes, are key players in maintaining a finely tuned pH balance between intra‐ and extracellular spaces, and therefore in cellular homeostasis. V‐ATPase is a housekeeping ATP‐driven proton pump highly conserved among prokaryotes and eukaryotes. This proton pump, which exhibits a complex multisubunit structure based on cell type‐specific isoforms, is essential for pH regulation and for a multitude of ubiquitous and specialized functions. Thus, it is not surprising that V‐ATPase aberrant overexpression, mislocalization, and mutations in V‐ATPase subunit‐encoding genes have been associated with several human diseases. However, the ubiquitous expression of this transporter and the high toxicity driven by its off‐target inhibition, renders V‐ATPase‐directed therapies very challenging and increases the need for selective strategies. Here we review emerging evidence linking V‐ATPase and both inherited and acquired human diseases, explore the therapeutic challenges and opportunities envisaged from recent data, and advance future research avenues. We highlight the importance of V‐ATPases with unique subunit isoform molecular signatures and disease‐associated isoforms to design selective V‐ATPase‐directed therapies. We also discuss the rational design of drug development pipelines and cutting‐edge methodological approaches toward V‐ATPase‐centered drug discovery. Diseases like cancer, osteoporosis, and even fungal infections can benefit from V‐ATPase‐directed therapies.