Naphthoquine phosphate is primarily used as an antimalarial agent, particularly in regions where malaria is endemic. It is often combined with other antimalarial drugs like artemisinin to enhance its efficacy and reduce the risk of drug resistance. The compound works by interfering with the parasite's ability to metabolize and utilize hemoglobin, ultimately leading to its death.

In clinical settings, it is administered orally and is known for its rapid action against Plasmodium species, including those resistant to other antimalarial drugs. It is also used in preventive measures for travelers visiting malaria-prone areas.

Outside of its antimalarial applications, research is ongoing to explore its potential in treating other parasitic infections and its role in combination therapies for enhanced therapeutic outcomes.