The introduction of Expanded Program on Immunization (EPI) and the availability of vaccines have contributed to significant reduction in morbidity and mortality rate, particularly among infants and children under five years. The coronavirus pandemic has however interrupted vaccination systems, limiting access and coverage for children. This study assesses the effect of the coronavirus disease outbreak on the EPI activities. The study employed a cross-sectional study design. Purposive and convenience sampling methods were used to sample 510 health workers directly engaged in immunization activities from 15 health care facilities. Coverages for five selected antigens (Diphtheria, Tetanus, Pertussis, Poliomyelitis, Tuberculosis) and Measles in the year 2020 experienced an overall decline ranging from 38.8% for measles rubella vaccine to 53.1% for Penta vaccine. The year 2019 recorded coverages ranging from 69.1% for BCG vaccine to 78.4% for penta vaccine, relatively higher than 2020. EPI services patronization rose up after COVID-19 peaks periods for BCG vaccine 67.7% to 89.2% for penta vaccine. The COVID-19 pandemic disrupted the delivery of EPI services significantly. Healthcare stakeholders can envisage telehealth services in care delivery against pandemic outbreaks. This study contributes to empirical knowledge by recommending vital predictive factors during a pandemic outbreak.