Objective: To identify differential effects of mild traumatic brain injury (TBI) occurring in a deployment or nondeployment setting on the functional brain connectome. Setting: Veterans Affairs Medical Center. Participants: In total, 181 combat-exposed veterans of the wars in Iraq and Afghanistan (n = 74 with deployment-related mild TBI, average time since injury = 11.0 years, SD = 4.1). Design: Cross-sectional observational study. Main Measures: Mid-Atlantic MIRECC (Mid-Atlantic Mental Illness Research, Education, and Clinical Center) Assessment of TBI, Clinician-Administered PTSD Scale, connectome metrics. Results: Linear regression adjusting for relevant covariates demonstrates a significant (P < .05 corrected) association between deployment mild TBI with reduced global efficiency (nonstandardized β = −.011) and degree of the K-core (nonstandardized β = −.79). Nondeployment mild TBI was significantly associated with a reduced number of modules within the connectome (nonstandardized β = −2.32). Finally, the interaction between deployment and nondeployment mild TBIs was significantly (P < .05 corrected) associated with increased mean (nonstandardized β = 9.92) and mode (nonstandardized β = 14.02) frequency at which connections occur. Conclusions: These results demonstrate distinct effects of mild TBI on the functional brain connectome when sustained in a deployment versus nondeployment context. This is consistent with findings demonstrating differential effects in other areas such as psychiatric diagnoses and severity, pain, sleep, and cognitive function. Furthermore, participants were an average of 11 years postinjury, suggesting these represent chronic effects of the injury. Overall, these findings add to the growing body of evidence, suggesting the effects of mild TBI acquired during deployment are different and potentially longer lasting than those of mild TBI acquired in a nondeployment context.