The best management strategy for HIV patients who fail to respond to first-line therapy for Pneumocystis jirovecii pneumonia is currently unclear. We identified all patients who were treated with trimetrexate and folinic acid who failed 7 or more days of cotrimoxazole, clindamycin-primaquine or dapsone-trimethoprim between 1996 and 2006. Trimetrexate was tolerated in 100% of cases with no treatment termination secondary to adverse drug reactions. Despite severe disease, 71% of patients were alive after 12 weeks.