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 (treatmentadjusted, 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 (ߠ11.36 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.