OBJECTIVES: Describe proportions of individuals with patellofemoral pain (PFP) with an unfavourable recovery over 12 months; identify clinical predictors of poor recovery at 3 and 12 months; and determine baseline values of predictors that identify those with poor 12-month prognosis. METHODS: An observational analysis utilised data from 310 individuals with PFP enrolled in two randomised clinical trials. Thirteen baseline variables (participant, PFP, study characteristics) were investigated for their prognostic ability. Pain, function and global recovery were measured at 3 and 12 months. Multivariate backward stepwise regression analyses (treatment-adjusted, p<0.10) were performed for each follow-up measure. Receiver operator characteristic curves identified cut-points associated with unfavourable recovery at 12 months. RESULTS: 55% and 40% of participants had an unfavourable recovery at 3 and 12 months, respectively. Longer baseline pain duration was significantly associated with poor 3-month and 12-month recovery on measures of pain severity (β 11.36 to 24.94), Anterior Knee Pain (AKP) Scale (-4.44 to -11.33) and global recovery (OR: 2.32 to 6.11). Greater baseline pain severity and lower AKP Scale score were significantly associated with poor recovery on multiple measures (p<0.05). Baseline duration >2 months and AKP Scale score <70/100 were associated with unfavourable 12-month recovery. CONCLUSIONS: A substantial number of individuals with PFP have an unfavourable recovery over 12 months, irrespective of intervention. Knee pain duration >2 months is the most consistent prognostic indicator, followed by AKP Scale score <70. Sports medicine practitioners should utilise interventions with known efficacy in reducing PFP, and promote early intervention to maximise prognosis. TRIAL REGISTRATION: Australian study: Australian Clinical Trials Registry (ACTRN012605000463673), ClinicalTrials.gov (NCT00118521); Dutch study: International Standard Randomised Controlled Trial Number Register (ISRCTN83938749).