We assessed the impact of pneumococcal conjugate vaccines on pneumococcal otitis media (OM) among children living in Navajo and White Mountain Apache Tribal lands. During the PCV7 era (2000-2009), the proportion of vaccine-type OM declined. However, vaccine-type OM (predominantly 3, 19A, and 19F) persisted in the PCV13 era (2010-2019).