This retrospective study aims to compare differences in the medical costs between inpatients infected/colonised with carbapenem-resistant (CRAB) and carbapenem-susceptible (CSAB) Acinetobacter baumannii in a hospital in Zhejiang province, China. Because the patient population was large, we randomly selected 60% of all inpatients with clinical specimens between 2013 and 2015. We classified the A. baumannii cases as CRAB or CSAB based on antibiotic susceptibility testing. Univariate and multivariate analyses were used to identify factors associated with the total medical cost (TMC). Those included in the study totalled 2980 inpatients, 71.3% of whom had CRAB infection/colonisation. Differences in the TMC between the CRAB and CSAB groups were lower by multivariate analyses than the differences obtained by univariate analyses. Carbapenem resistance was significantly associated with an approximately 1.5-fold increase in the TMC after accounting for confounding factors. Our study highlights the heavy financial burden imposed by A. baumannii and carbapenem resistance on the Chinese healthcare system.