Laboratory-based influenza surveillance was conducted in the 2019-2020 influenza season among Department of Defense (DoD) beneficiaries through the DoD Global Respiratory Pathogen Surveillance Program (DoDGRS). Sentinel and participating sites submitted 28,176 specimens for clinical diagnostic testing. A total of 5,529 influenza-positive cases were identified. Starting at surveillance week 45 (3-9 November 2019), influenza B was the predominant influenza type, followed by high activity of influenza A(H1N1)pdm09 three weeks thereafter. Both influenza B and influenza A(H1N1)pdm09 were then highly co-circulated through surveillance week 13 (22-28 March 2020). End-of-season influenza vaccine effectiveness (VE) was estimated using a test-negative case-control study design. The adjusted end-of-season VE for all beneficiaries, regardless of influenza type or subtype, was 46% (95% confidence interval: 40%-52%). The influenza vaccine was moderately effective against influenza viruses during the 2019-2020 influenza season.