High vaccine coverage at the district level may not translate with the same vigor to subdistrict levels; therefore, it is important to understand coverage inequalities. This study underscored vaccine coverage inequalities at subdistrict levels and explored reasons for immunization failure in a high-performing rural district of Pakistan. Parents of children aged 12 to 23 months were randomly selected and interviewed for child’s vaccination history through a cross-sectional survey in 2008. Using secondary data (GIS maps and population census), coverage was plotted in respect to sociodemographic and presence of lady health workers. The proportion of children fully immunized was found notably low (75%) than officially reported (85%). Coverage inequalities were observed at subdistrict levels, ranging from 58% to 85% in rural to urban areas and from 60% to 80% in lower to higher income quintiles. Distance to immunization facility, parental unawareness, and wrong ideas about vaccination were statistically significant for immunization failure. Focus of immunization microplans at the subdistrict level are needed to achieve universal immunization goals.