Patellofemoral pain (PFP) is a common complaint among young sports active adolescents. This study evaluated the longitudinal changes in pro-nociceptive and anti-nociceptive mechanisms in young adolescents with PFP, their impact on prognosis and responsiveness to treatment. Adolescents (N=151, aged 10-14 years) diagnosed with PFP were compared to age-matched controls (N=50) and subsequently tracked while participating in an intervention focussed on activity modification. They underwent quantitative sensory testing at baseline (pre-intervention), four weeks (during initial treatment), and twelve weeks (following treatment). Pressure pain thresholds (PPTs) were recorded on the knee, shin and elbow. Temporal summation of pain (TSP) was assessed by the increase in pain intensity during ten repeated cuff pressure pain stimulations on the leg. Conditioned pain modulation (CPM) was defined as change in cuff pain thresholds on one leg, during painful cuff conditioning on the contralateral leg. At baseline, adolescents with PFP had decreased PPTs at the knee, shin and elbow (P<0.001) as well as more facilitated TSP (P<0.05) compared with controls. For CPM at baseline, controls displayed an increase in cuff pain thresholds during conditioning (P<0.05), while those with PFP did not. More facilitated baseline TSP was associated with less improvements in pain intensity during the intervention (P<0.01). PPTs increased at both follow-ups (P<0.001), and the PPT-increase were associated with decreases in pain intensity (r=0.316; P<0.001). Overall, TSP remained facilitated at follow-ups, and there was no change in CPM. This is the first study to demonstrate a pro-nociceptive mechanism as a prognostic factor in young adolescents with PFP.