Abstract Background Routine Immunisation (RI) is critical in mitigating child morbidity and mortality while preventing the spread of infectious diseases. Nevertheless, the COVID-19 pandemic has resulted in considerable disruptions, which have given rise to an unprecedented number of zero-dose (ZD) infants. It has presented formidable obstacles for healthcare systems on an international scale. Methods The study employed a retrospective analysis of data obtained from thirteen Supplementary Immunisation Activities (SIAs) that were carried out from 2019 to 2021 to investigate the fluctuations in the documented number of children with ZD. Health authority stakeholder interviews yielded valuable insights about vaccination strategies and obstacles. Results An enormous increase in the number of documented ZD minors were identified during the study period. The number of documented ZD minors rose from 3,827 in 2019 to 4,271 in 2020, and then again to 9,620 in 2021. Notwithstanding diligent attempts to immunise ZD children, the vaccination rate persisted at a less-than-ideal 81.24% of documented ZD children in 2021. Conclusions As a result of the COVID-19 pandemic, pre-existing obstacles to accessing ZD infants in Islamabad were further intensified. The lessons learned emphasise the significance of community engagement, improved outreach strategies, and fortified healthcare infrastructure in guaranteeing comprehensive immunisation coverage. It is imperative to confront these challenges to reduce the likelihood of subsequent epidemics and protect children’s health. Key messages • The spread of COVID-19 among ZD neonates in Islamabad accelerated, prompting calls for improved vaccination programmes. • The suboptimal ZD vaccination rate in 2021, despite concerted efforts, underscores the criticality for enhanced strategies.