Background: Patellofemoral pain syndrome (PFPS) is known as one of the most frequent knee diseases and is the most frequent cause of anterior knee pain. Despite the high prevalence of the disease, its predisposing factors are not clearly known. Neuromuscular control disorders of hip and lumbopelvic complex and instability of core redounds to instability of whole movement pack chain. The aim of the present was to comparing the electromyographic activities of core muscles and muscles around the knee joint during gait in patients with PFPS with healthy subjects. Methods: This descriptive-analytic case-control study was carried out in School of Rehabilitation in Shahid Beheshti University of Medical Sciences, Tehran, Iran. The present study was carried out during 10 months (April to February in 2016). Thirty-two subjects containing 17 patients with patellofemoral pain syndrome (10 females and 7 males) and 18 healthy subjects (10 females and 8 males) participated in this study. In both groups the electrical activities of some of the muscles around the knee joint and the core muscles containing vastus medialis (VM), adductor longus (AL), gluteus maximus (G Max), external oblique abdominis (EOA), internal oblique abdominis (IOA), transverse abdominis (TA) and multifidus (M) were recorded during gait. Onset and offset time, duration and intensity of muscles activities were compared between two groups. Results: The results of the study showed that duration and intensity of the electrical activity of the gluteus maximus (respectively P=0.03, P=0.035) and offset time of electrical activity of the internal oblique abdominis (P=0.04) and the transverse abdominis (P=0.03) during gait, were significantly different between two groups. The external oblique abdominis and the multifidus electrical activities had not any significant differences between two groups (P>0.05). Conclusion: It seems that electromyographic activities of some of core muscles in patients with patellofemoral pain syndrome in comparison with healthy subjects are different. However, there was no differences in electromyographic activities in some of the muscles around the knee between patients and healthy subjects.