Despite having number of health benefits, yoga also has a proven role in enhancing performance of athletes boosting specific components of fitness. Our aim was to study the effect of yoga on flexibility and balance among shooting trainee athletes at BKSP, Bangladesh. A quasi-experimental study was conducted among shooting trainee athletes. In total 20 athletes took part in this study. In each group we had 10 participants (10 in yoga group and other 10 in non-yoga group). Regular yoga session have been conducted early morning biweekly over a period of six weeks. All the participants were allowed to take part in regular training session, while only yoga group took part in additional yoga session. Measurements of flexibility and balance including Sit and Reach (SR) test and Stork Stand (SR) test were taken immediately before and after the yoga training period. Independent t-test and paired t-test were used to determine the significant effect of yoga within and between the groups before and after yoga training. Sixty percent of our participants were male. Participant’s age were between 12-17 years. All of them had normal level of BMI. Significant improvement were observed in the yoga group for flexibility (SR, P=0.017) and balance (SS, P=0.004) during within group comparison. No significant improvement were seen for flexibility and balance in the non-yoga group. Between group comparison (Yoga and Non-yoga) also shows significant enhancement in both flexibility (SR, P=0.018) and balance (SS, P=0.021).Our findings helped us to conclude that regular yoga training may improve the balance and flexibility of shooting athletes even within short period of time (6 weeks), can also improve the athletic performances that demands high flexibility and balance.