Background: Patellofemoral joint (PFJ) is frequently affected in runners as when it is subjected to overload; puts stress on the joint by increasing the pressure points and leading to pain. Eccentric training is essential in strengthening weak muscles. Pilates improves flexibility and strengthen muscles strengthening whole body muscles and improve function especially in runners. Hence our project aims to find out which one of the two exercise forms targeted to PFJ, results in greater improvements in pain and physical function. Methods: After ethical approval 66 participants were involved in the project, Eccentric (n=34) and Pilates (n=32). Anterior knee pain scale and KOOS questionnaire were used as outcome measures. Statistical analysis was done using in stat. Results: AKPS and KOOS both showed significant improvements (P<0.001) when compared within the groups. When compared between two groups for pain it showed significant p–value– 0.004 showing that eccentric training plays a better role in reducing pain. However, when compared between two groups for functions, p value – 0.530 indicates that both groups are equally effective in improving functions. Conclusion: Our study shows that eccentric strengthening gave greater results in improving pain within six weeks. However, the functions have equally improved with both the groups.