Background: Patellofemoral pain (PFP) significantly affects patients’ daily activities and consequently reduces their quality of life. Custom-made foot orthoses (FOs) are a common method of medical treatment that positively influences biomechanical factors such as the kinematics of the lower extremity and reduces pain perception in patients. However, there is a gap in research regarding the influence of different FO treatments on knee pain. Therefore, this study addresses the impact of biomechanical foot orthoses (BMFOs) and sensorimotor foot orthoses (SMFOs) on patients with foot deformity and PFP. Methods: A total of 26 participants (9 men, 17 women; 27.7 ± 10.7 years; 175.0 ± 0.1 cm; 75.7 ± 18.8 kg; BMI: 24.7 ± 5.6) took part in this randomized controlled clinical trial. In the pre-test, knee pain was evaluated using the Kujala Anterior Knee Pain Scale after the physician’s anamnesis and plantar pressure measurement. A 3-month intervention with SMFO and BMFO was performed, and weekly development was evaluated using 11-item visual analog scales (VASs). Repeated measures analyses of variance were used to assess differences between time of measurements (ToMs) and the interaction effect between ToMs and treatment groups (SMFO, BMFO). Results: Statistical analysis revealed no statistically significant interaction between ToMs and treatment groups but a significant main effect on Kujala anterior knee pain scores (MDiff = 10.189; p = 0.014) and 12-week VAS (p = 0.001). Conclusions: The findings indicate that both treatment approaches effectively alleviated perceived knee pain in the PFP sample with foot deformity, with neither approach demonstrating superior efficacy. This trial was registered in the WHO International Clinical Trials Registry Platform (ICTRP) and German Clinical Trials Register (DRKS00035082).
