The premenstrual syndrome (PMS) comprises various physical and emotional symptoms which are associated with the menstrual cycle. The emotional changes might be due to the variation in the levels of BDNF especially lower levels of plasma BDNF may be present at the luteal phase of menstrual cycle. To date, no data were present to associate the link between BDNF gene polymorphism and PMS among young Menarcheal females. So, the goal of this investigation is to find out the possible relationship between BDNF gene polymorphism and PMS among young Menarcheal females of Pakistan. A total of 92 menarcheal girls with age range of 11-14yrs met the inclusion criteria. All participants were screened for the depression and PMS using Zung’s depression scale/ Diagnostic and Statistical Manual of Mental Disorders-IV (DSM IV) criteria and world health organization (WHO) criteria for PMS respectively. Genomic DNA was extracted from oral samples by Salting out method and BDNF genotyping was done using PCR-RFLP analysis. Results showed no significant association (χ2=1.685, p-value=0.431) was observed between BDNF genotyping and PMS among menarcheal girls. BDNF (rs6265) AA and GA genotypes did not show significant association with the risk of PMS. Hence, it was concluded that BDNF gene polymorphism may not be associated with the PMS among Pakistani Menarcheal girls