This study examined the impact of Japanese encephalitis (JE) immunization policies on disease trends in China. Through a document review and key source interviews in eight provinces, the study found, JE immunizations were provided via a combination of fee-for-service and government funding. Unequal government funding and unbalanced economic development led to variation in JE incidence levels between provinces. Government support of low-fee JE immunization, has led to nationwide decline of JE incidence by >90%; however, greater reliance on user fees and market mechanisms in rural areas has limited the provision of JE and other childhood immunizations to poor rural children.