Treatment for PCP involves the use of antibiotics. These include trimethoprim-sulfamethoxazole (TMP-SMX, Bactrim, Septra) and pentamidine isoethionate (Nebupent, Pentam 300). Both of these anti-microbial drugs are equally effective. AIDS patients are typically treated for 21 days, whereas non-AIDS patients are treated for 14 days. TMP-SMX may be highly toxic in AIDS patients, causing severe side effects that include fever, rash, decreased numbers of white blood cells and platelets, and hepatitis. Pentamidine also causes side effects in immunocompromised patients. These side effects include decreased blood pressure, irregular heart beats, the accumulation of nitrogenous waste products in the blood (azotemia), and electrolyte imbalances. Pentamidine can be given in aerosol form to minimize side effects. Alternative drugs can be used for patients experiencing these side effects.

P. carinii appears to be developing resistance to TMP-SMX. In addition, some patients are allergic to the standard antibiotics given for PCP. As a result, other antibiotics for the treatment of PCP are continually under investigation. Some drugs proven to be effective against P. carinii include dapsone (DDS) with trimethoprim (Trimpex), clindamycin (Cleocin) with primaquine, as well as atovaquone (Mepron). Paradoxically, corticosteroids have been found to improve the ability of TMP-SMX or pentamidine to treat PCP. As a treatment of last resort, trimetrexate with leucovorin (Wellcovorin) can also be used.