Overweight and obesity prevalence has increased over the past 30 years. Few studies have looked at the enrolled Military Health System (MHS) population (2.2 million per year). This descriptive study examined trends in overweight and obesity in both children and adults from fiscal years 2009 to 2012 and compared them to the U.S. population. Prevalence in MHS children decreased over time for overweight (14.2-13.8%) and obesity (11.7-10.9%). Active duty adults showed an increase in overweight prevalence (52.7-53.4%) and a decrease in obesity prevalence (18.9-18.3%). For nonactive duty, both overweight and obesity prevalence remained relatively unchanged around 33%. For both children and adults, overweight and obesity prevalence increased with age, except for obesity in the nonactive duty ≥ 65 subgroup. When compared to the United States by gender and age, MHS children generally had a lower overweight and obesity prevalence, active duty adults had higher overweight and lower obesity prevalence, and nonactive duty adults had comparable overweight and obesity prevalence, except for obesity in both men in the 40 to 59 subgroup and women in ≥ 60 subgroup. More research on the MHS population is needed to identify risk factors and modifiable health behaviors that could defeat the disease of obesity.