High rates of sexually transmitted infections (STIs), including Chlamydia trachomatis (CT), have been documented among U.S. military service members. However, it is unknown whether phases of the deployment cycle affect risk for CT. This article characterizes the rates of CT infections during the predeployment, deployment, and post-deployment phases for active component members of the U.S. Army, Navy, Air Force, and Marine Corps during 2008-2015. Cases of CT were defined using laboratory, reportable medical event, and prescription data in a sensitivity analysis approach. Adjusted incidence rate ratios for CT were calculated using a multivariable Poisson model. In these analyses, the crude and adjusted incidence rates of CT were found to be highest during the pre-deployment phase for both sexes. However, men's rates of CT differed only slightly across pre-, post-, and non-deployed phases, while women had substantial rate differences between phases. These analyses call for better screening and documentation of STIs during deployment, as well as continued surveillance of STIs in the Military Health System, to assess the true burden of disease.