OBJECTIVES: To estimate the prevalence of zero dose children (who have not received any dose of pentavalent (diphtheria, tetanus, pertussis, type B and hepatitis B) vaccine by their first birthday) among those who interacted with the immunisation system in Sindh, Pakistan along with their sociodemographic characteristics and risk factors. DESIGN AND PARTICIPANTS: We conducted a descriptive analysis of child-level longitudinal immunisation records of 1 467 975 0-23 months children from the Sindh's Zindagi Mehfooz (Safe Life) Electronic Immunisation Registry (ZM-EIR), for the birth cohorts of 2017 and 2018. SETTING: Sindh province, Pakistan which has a population of 47.9 million people and an annual birth cohort of 1.7 million. PRIMARY AND SECONDARY OUTCOME MEASURES: The primary outcome measure was zero dose status among enrolled children. Logistic regression was performed to identify the risk factors associated with the zero dose status. RESULTS: Out of 1 467 975 children enrolled in the ZM-EIR in Sindh, 10.6% (154 881/1 467 975) were zero dose. There were sharp inequities across the 27 districts. Zero dose children had a lower proportion of hospital births (28.5% vs 34.0%; difference 5.5 percentage points (pp) (95% CI 5.26 to 5.74); p<0.001) and higher prevalence from slums (49.5% vs 42.3%; difference 7.2 pp (95% CI 6.93 to 7.46); p<0.001), compared with non-zero dose children. Children residing in urban compared with rural areas were at a higher risk (relative risk (RR): 1.20; p<0.001; 95% CI 1.18 to 1.22), while children with educated compared with uneducated mothers were at a lower risk of being zero dose (RR: 0.47-0.96; p<0.001; 95% CI 0.45 to 0.98). CONCLUSIONS: Despite interacting with the immunisation system, 1 out of 10 children enrolled in the ZM-EIR in Sindh were zero dose. It is crucial to monitor the prevalence of zero dose children and investigate their characteristics and risk factors to effectively reach and follow-up with them.