OBJECTIVES: This study evaluated the effects of unmodified prefabricated foot orthoses over a 12-week period on functional performance; and subjective pain and function in individuals with patellofemoral pain syndrome (PFPS). DESIGN: Prospective cohort study over 12 weeks. Each participant was prescribed prefabricated foot orthoses at baseline. PARTICIPANTS: Sixty individuals with PFPS (18-35 years). MAIN OUTCOME MEASURES: Change in pain and ease of completing a single leg squat; change in the number of pain free step downs and single leg rises from sitting; usual and worst pain in the previous week; the anterior knee pain scale (AKPS); and the lower extremity functional scale (LEFS). RESULTS: At 12 weeks, significant improvements in single leg squat pain and ease, and the number of pain free step downs and single leg rises from sitting were found. Additionally, significant reductions in usual and worst pain, and improvements on the AKPS and LEFS were observed. CONCLUSIONS: Functional performance improvements following unmodified prefabricated foot orthoses were greater at 12 weeks that those achieved immediately. Enhanced functional performance over time may have significant implications for osteoarthritis prevention in some individuals with PFPS. Improvements in subjective pain and function appear to plateau over time.