The pentavalent is a vaccine against Diphtheria, Pertussis, Tetanus, Hepatitis B, and Haemophilus type B influenza. A child is considered a pentavalent vaccination dropout if they have received the first dosage as advised but have not obtained the third dose. In Tanzania, the first-dose receiver of pentavalent was approximately 97 %, whereas only 89 % received a third dose. Unfortunately, no studies have been done in Tanzania to evaluate the factors at the national level that are linked with first-versus third-dose pentavalent vaccine dropout; hence, we explored these factors here for the first time. A cross-sectional survey of randomly selected households was conducted. The sample size was calculated to provide overall, age- and sex-specific coverage estimates for measles-rubella vaccine evaluation among children aged between 9 and 59 months at the national level, as explained elsewhere. The fieldwork activities were done for one month from November to December 2019 for both Zanzibar and Tanzania Mainland. A total of 4460 caregivers of children aged 12–23 months were interviewed for routine immunization services, and a total of 4403 caregivers were included in this analysis of the uptake of the pentavalent vaccine. The number of children who received the first dose of the pentavalent vaccine was 4020 (91.5 %), while the number of children who received the third dose of the pentavalent vaccine was 3915 (89.4 %). The overall pentavalent vaccination dropout rate was 2.3 %. The rate was lower in Zanzibar (0.9 %) than in the Tanzanian mainland (2.4 %). Wealth quintile, sex of caregivers, and education were factors significantly associated with the pentavalent-3 dropout rate among children aged 12–23 months in Tanzania. Our results provide strong support for further efforts to improve current vaccination coverage to optimize the use of prioritized, timely, and appropriate interventions at the regional and district levels and to improve the health education given to expectant women during their clinic visits so they may comprehend the value of routine immunization.