We aimed to estimate the socioeconomic burden of pneumonia due to multidrug-resistant Acinetobacter baumannii (MRAB) and Pseudomonas aeruginosa (MRPA).We prospectively searched for MRAB and MRPA pneumonia cases and matched them with controls with susceptible-organism pneumonia and non-infected cases from ten hospitals over a 6-month period. The matching criteria were: same principal diagnosis, same surgery or intervention during hospitalization, age (years ± 10), sex, and admission date within 60 days. The total additional direct medical cost was estimated by the multistate model. A total of 108 cases of MRAB pneumonia [MRAB-P] and 28 cases of MRPA pneumonia [MRPA-P] were identified. The 90-day mortality rate was 37.0% and 39.3% for MRAB-P and MRPA-P, respectively. The additional medical costs were $42,203 and $35,556 for MRAB-P and MRPA-P, respectively. The estimated number of MRAB-P and MRPA-P cases were 1,309–2,483 and 339–644, respectively with estimated deaths being 485–920 and 133–253 in a year, respectively. The annual socioeconomic burden was $12,053,593–$22,898,271 and $15,241,883–$28,994,008, respectively. We estimated that MRAB-P and MRPA-P occurred in 1,648–3,172 patients, with 618–1,173 deaths, and caused $27,295,476–$51,892,279 in socioeconomic burden nationwide. It is time to investigate and invest in prevention of multidrug-resistant bacterial pneumonia.