Patellofemoral pain syndrome) PFPS) is one of the most common knee injuries at a young age and is more common in women. Because of pain, muscle weakness and proprioception loss of in knee, these people have a deficit balance. The purpose of this study was Comparison of Land-based physical therapy with Aquatic physical therapy to improvement pain, physical function, static and dynamic balance in patient with PFPS. In this present quasi-experimental study twenty patients with PFPS participated and were divided into two groups: physical therapy on land and water. Subjects in both groups performed three sessions of exercise therapy per week for 8 weeks. In the beginning and at the end of the period, the patients' pain, function, static and dynamic balance respectively was assessed by visual analogue scale, kujala score, sharpend Romberg and star excursion balance test. Data was analyzed using SPSS (version 18) at a significance level of (P ≤ 0.05). In this study, pain, function, static and dynamic balance scores of the both groups significantly improved after the exercise period (P ≤ 0.05). However, there was no significant difference of data between the two groups in pain, function, static and dynamic balance (P ≥ 0.05). The results showed that physical therapy in water and land can be used as a useful and effective method to reduce pain, improve function, static and dynamic balance of PFPS patients. Although the results did not show statistically significant differences between the two groups the difference between two groups in the mean percentage change indicates that the clinical effect of exercise in water is higher than the land. According to these results aquatic physical therapy is recommended as an effective method for the treatment of patients with patellofemoral pain syndrome.