The treatment of carbapenem-resistant Enterobacteriaceae (CRE) is diverse in each region due to the difference in local resistant patterns of CRE. We aimed to explore how physicians in Thailand decide on selection options for treating CRE infections. In this study, 25 physicians who were not infectious disease (ID) specialists participated in this semi-structured in-depth interview. We found that they, in general, did not provide empiric antibiotics for the treatment of CRE. However, some patients, e.g., those with prior carbapenems exposure may have brought CRE to physicians’ attention. ID specialists played critical roles in both empiric and specific CRE treatment. There were multiple scenarios when CRE management deviated from recommendations, especially when physicians perceived that the evidence that supported the recommendations was weak. Several supportive factors, challenges, and improvements were also suggested. In conclusion, ID specialists, adequate information, and consistent implementation of infectious control policy are crucial to the treatment and prevention of CRE infection.