Japanese encephalitis (JE) is a flavivirus endemic to regions in Asia and the Western Pacific. JE vaccination (3-dose series ≤2011, 2-dose series ≥2009) is an inactivated vaccine required among US service members deployed to and stationed in JE endemic regions. The current JE vaccination formulation in the United States has been shown to be safe in pregnancy through animal models, but epidemiologic studies are lacking. We conducted a descriptive analysis to determine the prevalence of JE vaccination in pregnancy among active duty military mothers. The study population included 163,596 pregnancies ending in live deliveries to military mothers from 2003–2014. Pregnancies were captured by the Department of Defense Birth and Infant Health Research program and linked to immunization records. Women who received JE vaccination in pregnancy were compared with those who did not. There were 446 mothers vaccinated in pregnancy: 415 in the first trimester and 31 in the second/third trimester. Of the mothers vaccinated in pregnancy, 231 (51.8%) received their first dose and 69 (15.5%) received >1 dose. Most mothers were vaccinated with the 3-dose (69.1%) versus 2-dose (30.9%) formulation. Vaccinated mothers were more likely to be younger, unmarried, in the Marines, enlisted rank, and in an occupation other than health care or combat. They were also more likely to have received other non-recommended vaccines in pregnancy. Understanding characteristics of women who receive JE vaccination in pregnancy may help guide future policy. The increasing number of military women makes vaccine safety in pregnancy a priority for protecting military families.