Flatfoot is linked to secondary lower limb joint problems, such as patellofemoral pain. This study aimed to investigate the influence of medial posting insoles on the joint mechanics of the lower extremity in adults with flatfoot. Gait analysis was performed on fifteen young adults with flatfoot under two conditions: walking with shoes and foot orthoses (WSFO), and walking with shoes (WS) in random order. The data collected by a vicon system were used to drive the musculoskeletal model to estimate the hip, patellofemoral, ankle, medial and lateral tibiofemoral joint contact forces. The joint contact forces in WSFO and WS conditions were compared. Compared to the WS group, the second peak patellofemoral contact force (p < 0.05) and the peak ankle contact force (p < 0.05) were significantly lower in the WSFO group by 10.2% and 6.8%, respectively. The foot orthosis significantly reduced the peak ankle eversion angle (p < 0.05) and ankle eversion moment (p < 0.05); however, the peak knee adduction moment increased (p < 0.05). The reduction in the patellofemoral joint force and ankle contact force could potentially inhibit flatfoot-induced lower limb joint problems, despite a greater knee adduction moment.