Background: Patellofemoral Pain Syndrome (PFPS) is a prevalent condition characterized by anterior knee pain, significantly affecting individuals' balance and proprioception. Despite its commonality, the relationship between PFPS and these functional impairments remains inadequately explored. Previous studies have suggested a link, but comprehensive analyses incorporating balance, proprioception, and PFPS are scarce. Objective: This study aimed to investigate the association between PFPS and deficits in balance and proprioception, emphasizing the potential for rehabilitation focused on these areas to improve patient outcomes. Methods: A cross-sectional study was conducted with 103 participants diagnosed with PFPS, utilizing non-probability convenience sampling at the Out-Patient Department of Physical Therapy, Akbar Medical Complex, Mardan, Pakistan. Participants underwent assessments for balance (using static and dynamic balance tests) and proprioception (via joint position sense testing). Data analysis was performed using SPSS version 22, with chi-square tests to assess statistical associations between PFPS and the measured variables. Results: Among the participants, 60.2% were males, and 39.8% were females, with an injured limb distribution of 30.1% for both the left and right legs and 39.8% for both legs. The duration of symptoms varied, with 51.5% experiencing symptoms for 1-3 months. Proprioception degree angles showed mean values of 37.5728 (SD=3.76933) for the right limb and 38.4272 (SD=5.81681) for the left limb. Chi-square tests revealed significant impairments in balance and proprioception among individuals with PFPS (p < 0.05). Conclusion: The study confirmed a significant association between PFPS and impairments in balance and proprioception. These findings support the integration of balance and proprioceptive training into rehabilitation programs for PFPS patients, potentially improving symptoms and functional outcomes.