Ligament reconstruction is indicated in patients with an isolated posterior cruciate ligament (PCL) injury who fail conservative treatment. To eliminate the need for PCL reconstruction, an ideal rehabilitation program is important for patients with an isolated PCL injury. The purpose of this study was to investigate the improvement in functional outcome, proprioception, and muscle strength after a Both Sides Up (BOSU) ball was used in a balance combined with strength training program in patients with an isolated PCL injury. Ten patients with isolated PCL injuries were recruited to receive a 12 week training program as a study group. In the control group (post-PCL reconstruction group), ten subjects who had undergone isolated PCL reconstruction for more than 2 years were enrolled without current rehabilitation. The Lysholm score, IKDC score, proprioception (active and passive), and isokinetic muscle strength tests at 60°/s, 120°/s, and 240°/s, were used before and after training on the injured and normal knees in the study group, and in the post-PCL reconstruction group. The results were analyzed with a paired t-test to compare the change between pre-training, post-training, and the normal leg in the study group, and with an independent t-test for comparisons between the study and post-PCL reconstruction groups. Both the Lysholm and IKDC scores were significantly improved (p < 0.01) after training, and no difference was observed compared to the post-PCL reconstruction group. The active and passive proprioception was improved post-training compared to pre-training, with no difference to that in the post-PCL reconstruction group. Isokinetic knee quadriceps muscle strength was significantly greater post-training than pre-training in PCL injured knees at 60°/s, 120°/s, and 240°/s, and in hamstring muscle strength at 60°/s and 120°/s. Muscle strength in the post-training injured knee group showed no significant difference compared to that in the post-training normal leg and the post-PCL reconstruction group. The post-training improvement of muscle strength was higher in the PCL injured leg compared to the normal leg and there was no difference between the dominant and non-dominant injured leg in the study group. After 12 weeks of BOSU balance with strength training in patients with an isolated PCL injury, the functional outcome, proprioception, and isokinetic muscle strength were significantly improved, and comparable to the contralateral normal leg and the post-PCL reconstruction group. We suggest that programs combining BOSU balance and strength training should be introduced in patients with a PCL injury to promote positive clinical results.