Atovaquone is primarily used as an antimalarial medication, often in combination with proguanil, to prevent and treat malaria caused by Plasmodium falciparum. It works by inhibiting mitochondrial electron transport, which disrupts the parasite's energy production. This makes it effective in areas where malaria is resistant to other treatments. Additionally, atovaquone is used to treat Pneumocystis jirovecii pneumonia (PCP), a serious infection that commonly affects individuals with weakened immune systems, such as those with HIV/AIDS. Its ability to target specific pathogens while having a relatively low toxicity profile makes it a valuable option in managing these infections.