CCD-based fluorescence tomography is widely used for small animal whole-body imaging. In this report, systematic signal-to-noise ratio (SNR) analyses of a fluorescence tomography imaging (FTI) system were performed, resulting in an easy-to-follow strategy to optimize hardware configurations and operational conditions for acquiring high-quality imaging data and for improving the overall system performance. Phantom experiments were conducted to demonstrate the performance improvement by these optimizations. The improved performance was further verified by imaging a tumor-bearing mouse in vivo. This report provides general and practical guidelines for setting up a high-performance electron multiplying charge coupled device based FTI system to achieve an optimized SNR, which can be useful for future FTI technology development.