Idiopathic anterior knee pain in teenagers and young adults is a common condition. Patellar maltracking has been considered as a causative factor. The aim of our study was to investigate whether there was a difference in the timing of electromyographic (EMG) activity in the medial and lateral hamstring and quadriceps muscles of patients with anterior knee pain compared to asymptomatic control participants. This was a cross sectional observational study measuring EMG activation patterns. Two groups of participants were tested, one patient (mean age 15 years, n=20) and one asymptomatic control (mean age 16 years, n=17). Surface EMG (sampling rate 1000 Hz) was recorded from vastus medialis obliqus, vastus lateralis, and the medial and lateral hamstrings during three repetitions of maximal voluntary isometric contractions. The relative timing of the medial and lateral quadriceps and hamstrings was evaluated. The mean (95% confidence interval) difference between the groups in the lateral–medial hamstring onset timing was 53.8(1.9 to 105.6)ms during the maximal contraction. An independent t test showed that this difference was statistically significant (p=0.043). The differences between the groups in the relative VMO to VL onset did not reach statistical significance. The results of this study suggest that the lateral hamstrings contract significantly earlier in patients with AKP compared to healthy controls for this small cohort. This altered activation pattern could produce external rotation of the tibia on the femur and cause lateral patella tracking.