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Background In Ethiopia, despite national immunisation programmes, many children do not complete recommended vaccines. Identifying determinants of incomplete immunisation is crucial for designing interventions and guiding policy. This study explored factors associated with incomplete immunisation among children aged 12–23 months in Koore Zone, Southern Ethiopia.Methods A community-based unmatched case-control study was conducted from April to May 2025, including 279 children—93 incompletely immunised cases and 186 fully immunised controls randomly selected from 10 kebeles. Structured, interviewer-administered questionnaires adapted from WHO and United Nations Children’s Fund tools collected data on sociodemographics, maternal healthcare utilisation and caregiver knowledge. Descriptive statistics summarised participant characteristics. Bivariable and multivariable logistic regression identified independent associated factors of incomplete immunisation, expressed as adjusted ORs (AORs) with 95% CIs.Results Overall, 42% of incompletely immunised children were born at home. Maternal illiteracy, rural residence and home delivery significantly increased the likelihood of incomplete immunisation (AOR 1.82, 4.0 and 2.30, respectively). Attendance at antenatal care (AOR 0.51), postnatal care (AOR 0.46) and adequate maternal knowledge of immunisation (AOR 0.30) were protective.Conclusion In Koore Zone, incomplete immunisation is driven by maternal education, rural residence, home delivery, maternal healthcare utilisation and caregiver knowledge. Strengthening maternal and child health services, improving community awareness and educating caregivers about vaccination schedules are vital strategies to enhance immunisation coverage and reduce vaccine-preventable diseases. These findings provide practical guidance for policy makers and public health practitioners in similar low-resource settings.