Purpose: The aim of this study was to investigate the effects of foot core training (FCT) on dynamic function and balance, in addition to exercises for strengthening and stretching of hip and knee muscles in females with patellofemoral pain (PFP). Methods: Twenty-eight females with PFP were randomized into foot core training (FCT, n = 13) and standardized exercise groups (EXE, n = 15). The Timed-Up&Go Test (TUG) was used for dynamic function and balance, and Y-Balance Test (YBT) was used for dynamic balance; performed at baseline and after 6 weeks of the exercise program. For the EXE exercise program, routine and widely used exercises for strengthening and stretching of hip and knee muscles were selected. For patients assigned to the FCT, a similar program was performed with the addition of FCT. Physiotherapist-supervised exercise sessions were scheduled 2 times per week for 6 weeks and performed as a home program on the other days of the week. Results: Both groups displayed decreases in TUG scores, whereas YBT scores increased in both groups. No significant group by time interaction and no between-group differences were found (P > 0.05). Conclusion: In conclusion, the results from this study indicate that the dynamic balance impairment is due to not only foot pronation but also the malalignment of knee biomechanics and pain in PFP patients. We believe that there may be a need for a longer training period to achieve improvements in PFP patients. Trail Registration: clinicaltrials.gov NCT03099512.