This study measured the meta-efficiency of 85 business incubator centers located in Seoul and Gyeonggi-do in 2016 using data envelopment analysis. This study also employed bootstrap truncated regression to analyze the relationship between the business incubators’ operational policies and meta-efficiency based on the CRS and VRS. The major aspects of this study are as follows. First, the average meta-efficiency of a business incubator center in Seoul is greater than that of a center in Gyeonggi-do. This result demonstrates that business incubator centers in Gyeonggi-do need strategic alternatives to maximize an incubator’s performance. Second, managers’ capabilities and educational levels supporting business incubator centers have positive effects on the meta-efficiency score, thus indicating a need to improve efficiency by adjusting resource allocation and incubator center capacity. This study’s findings suggest strategic operational plans to cope with the fluctuations in the internal and external environments and to identify the best-practice business incubator centers that others can emulate. Furthermore, the results may help practitioners understand the business incubator centers’ environment from an operator’s perspective as well as offer strategic initiatives for efficient operation management.