This study details a one-time ray-tracing optimization method for the optimization of LED illumination systems [S.-C. Chu and H.-L. Yang, "One-time ray-tracing method for the optimization of illumination system," in Proceedings of International Conference on Optics in Precision Engineering and Nanotechnology (icOPEN, 2013), 87692M]. This method optimizes the performance of illumination systems by modifying the light source's radiant intensity distribution with a freeform lens, instead of modifying the illumination system structure. Because illumination system structures are unchanged in the design process, a designer can avoid the common problems faced when designing illumination systems, i.e., the repeated and time-consuming ray-tracing process when optimizing the illumination system parameters. The easy approaches of the proposed optimization method to sample the target illumination areas and to divide the light source radiant intensity distribution make the proposed method can be applied to both direct-lit and non-direct-lit illumination systems. To demonstrate the proposed method, this study designs an illuminator for a tube photo-bioreactor using the proposed one-time ray-tracing method. A comparison shows that in the designing of the photo-bioreactor, tracing all rays one time requires about 13 hours, while optimizing the light source's radiant intensity distribution requires only about twenty minutes. The considerable reduction in the ray-tracing time shows that the proposed method is a fast and effective way to design illumination systems.