Objectives: Although overuse running injury risks for the ankle and knee are high, the effect of different shoe designs on Achilles tendon force (ATF) and Patellofemoral joint contact force (PTF) loading rates are unclear. Therefore, the primary objective of this study was to compare the ATF at the ankle and the PTF and Patellofemoral joint stress force (PP) at the knee using different running shoe designs (forefoot shoes vs. normal shoes). Methods: Fourteen healthy recreational male runners were recruited to run over a force plate under two shoe conditions (forefoot shoes vs. normal shoes). Sagittal plane ankle and knee kinematics and ground reaction forces were simultaneously recorded. Ankle joint mechanics (ankle joint angle, velocity, moment and power) and the ATF were calculated. Knee joint mechanics (knee joint angle velocity, moment and power) and the PTF and PP were also calculated. Results: No significant differences were observed in the PTF, ankle plantarflexion angle, ankle dorsiflexion power, peak vertical active force, contact time and PTF between the two shoe conditions. Compared to wearing normal shoes, wearing the forefoot shoes demonstrated that the ankle dorsiflexion angle, knee flexion velocity, ankle dorsiflexion moment extension, knee extension moment, knee extension power, knee flexion power and the peak patellofemoral contact stress were significantly reduced. However, the ankle dorsiflexion velocity, ankle plantarflexion velocity, ankle plantarflexion moment and Achilles tendons force increased significantly. Conclusions: These findings suggest that wearing forefoot shoes significantly decreases the patellofemoral joint stress by reducing the moment of knee extension, however the shoes increased the ankle plantarflexion moment and ATF force. The forefoot shoes effectively reduced the load on the patellofemoral joint during the stance phase of running. However, it is not recommended for new and novice runners and patients with Achilles tendon injuries to wear forefoot shoes.