We have demonstrated the highest long-pulse efficiency and highest Q-switched energy reported to date for a Yb:S-FAP laser. THe Yb:S-FAP laser was pumped with a flashlamp pumped, free-running Cr:LiSAF laser. Threshold pump energy was extremely low, typically 30 mJ. Maximum output energy was 370 mJ at 1.047 micrometers with 650 mJ of pump incident on the Yb:S-FAP crystal. We obtained total optical-to-optical conversion efficiency of up to 57 percent in the long pulse mode. This is the highest conversion efficiency ever reported for this material in high energy, pulsed mode. Three samples of Yb:S-FAP of differing dimensions, doping, and crystal quality were tested. Two of the Yb:S-FAP crystals showing crystal defects experienced bulk damage during Q-switched mode of operation. The remaining crystal had the lowest dopant concentration of all the crystals, limiting the stored energy. Up to 65 mJ of output was obtained in this high-quality crystal, the highest ever reported in Q-switched mode with this laser material. Conversion efficiency at this energy level was 11.8 percent. However, the maximum efficiency obtained was 16.3 percent before pump bleaching effects started to occur due to low dopant concentration in this crystal sample.