X-ray breast computed tomography (breast CT) was developed by some research groups to overcome the limitations of mammography. Breast CT is expected to be an effective diagnostic tool because it can generate three-dimensional images of a breast. However, the spatial resolution of the existing system is not satisfactory for identifying microcalcifications within the breast. The purpose of this study was to develop a prototype of high-resolution breast CT system, and to evaluate the imaging properties of the developed system. Our experimental system consists of a microfocus X-ray tube and a flat panel detector with a C-arm frame, a bed, and their controllers. Images were reconstructed by using cone-beam X-ray projections and the Feldkamp-Davis-Kress algorithm. We used phantoms to experimentally evaluate three imaging properties and exposure dose. Consequently, the modulation transfer function value was 0.1 at the frequency of 6.0 LP/mm, which is higher than that of clinical CT and breast CT. Breast phantom microcalcifications were observed clearly. Furthermore, entrance surface dose in the experimental system was similar to that of mammography. These results indicate that our experimental system overcomes the limitations of both the mammogram and existing breast CT systems.