Vaccination uptake in the Federation of Bosnia and Herzegovina (FBiH), in Bosnia and Herzegovina, is suboptimal. This study aimed to (1) assess vaccination coverage, timeliness and drop-out for children born in 2015 and 2016 and compare these with official administrative coverage estimates, (2) identify associations between characteristics of children/caregivers and vaccination uptake. This was a cross-sectional study based on patient files for children 12-23 months (n = 1800) and 24-35 months (n = 1800). Methods were adapted from the World Health Organization cluster survey methodology. A two-stage stratified sampling procedure was conducted in urban and rural strata. A structured paper-based form was completed by a pediatrician/nurse from randomly selected primary care centers and patient files. Estimates were based on weighted analysis with a 95% confidence interval to account for the survey sampling design. Vaccination coverage was consistent with administrative coverage levels for BCG, DTP and MMR, and lower for HepB; all considerably lower than regional targets. Children in urban areas had lower vaccination uptake. An assumption that anti-vaccination sentiment prevails among caregivers was not confirmed; only 2% of children were not vaccinated at all, instead challenges related to delays and drop-out. An assumption of caregiver concerns for the MMR vaccine was confirmed with low uptake and delays. The FBiH has experienced vaccination schedule changes due to supply issues; findings confirmed that sustainability in supply and schedule is high priority. These data are new and provide important information for developing strategies to increase uptake.