The Expanded Program on Immunization (EPI) was created to scale up immunization of infants, but there have still been records of insufficient levels of immunization against childhood diseases in under-developed countries. Missed opportunity for vaccination is a strategy of achieving immunization coverage of at least 90% by reducing the process that facilitates it being missed and improving health service delivery in under-developed countries like Nigeria. The main objective of the study was to determine the level of missed opportunities in childhood routine immunization in Benin City, Edo State. A cross-sectional study design was utilized for this study in Primary Health Care facilities across the three Local Government areas in Benin city using a multistage sampling technique. The questionnaire was a pretested structured WHO tool, that was interviewer administered. Four hundred and seventy-seven of the children were aged 5 months or less, 20.5% of the children were in the age bracket aged 6-11 months, while only 5 children were aged 18-23 months (0.8%). The mean age of the children was 4.2 ± 3.5 months. The mean age of the male children was 4.4 ±3.5 months, while the mean age of the female was 3.9 ± 3.2 months. In conclusion, missed opportunity for vaccination in this study was high (16.1%) and this can lead to increase in vaccine preventable diseases.