Background: Normal levels of ghrelin and insulin hormones play an important role in energy-balance, weight control and preventing type 2 diabetes. The purpose of this study was to evaluate the effects of twelve weeks physical activity with omega-3 supplementation consumption on insulin and ghrelin hormones in young women. Materials and methods: In this semi-experimental study 60 young women aged 19-25 years randomly divided into four groups including. (Exercise with supplementation, exercise alone, supplementation alone and control group). Exercise group and exercise- supplementation group followed the basketball training for 12 weeks under the supervision of skillful trainers. Supplementation group and exercise- supplementation group were asked to take 3gram omega-3 capsules per day for 12 weeks. Anthropometric indicators and blood samples were obtained in the morning after an 8-12 hr fast prior to the start of the study and again 12weeks after at the end of the study under the same conditions to measure plasma ghrelin and insulin hormones (Elisa method). Data analysis using tests of Kolmogorov-Smirnov t-test, one-way analysis of variance (ANOVA) conducted through SPSS-16 software. Results: The results of ANOVA test showed that after 12 weeks of study ghrelin and insulin levels in exercise-supplement group, (P=0.000, P=0.000), exercise group (P=0.000, P=0.000), and supplement group (P=0.044, P=0.017) significantly increase and decrease respectively. But no significant changes were observed in control group for ghrelin (P=0.740) and insulin (P= 0.108) levels before and after the study. Conclusion: Based on the results of this study, physical activity with omega-3 supplementation can create significant changes on the levels of ghrelin and insulin hormones in young women. These changes may help to control and prevent diabetes and its, complications.