Background Neural tube defects (NTDs) are preventable congenital malformations that disproportionately affect low and middle income countries and contribute to disability and mortality. Evidence on the long-term outcomes of children and adolescents with NTDs in Eastern Africa has not been comprehensively synthesised. We conducted a systematic review and meta-analysis to assess survival, complications, and functional outcomes among children with NTDs in this region. Methods We searched PubMed, MEDLINE (Ovid), Cochrane Library, Web of Science, and Africa Index Medicus from the earliest records to April 2025. Two reviewers independently screened studies, assessed quality, and extracted data. We included studies reporting outcomes beyond one year of age, except mortality, which was assessed from birth onwards. Random-effects meta-analyses were undertaken when at least two sufficiently studies were available; otherwise, findings were synthesised narratively. Results Of 597 articles screened, 16 studies involving 2,340 children with NTDs met the inclusion criteria. Pooled cumulative mortality was 23% (95% CI: 12 - 36%) in the neonatal period, 9% (95% CI: 2 - 33%) during infancy, 22% (95% CI: 16 - 28%) in toddlers, 37% (95% CI: 30 - 44%) in pre school aged children and 45% (95% CI: 36 - 54%) in school-aged children. The pooled prevalence of hydrocephalus was 41% (95% CI: 34 - 48%) with little variation by age. Neurogenic bladder increased from 53% (95% CI 49 - 81%) in toddlers to 83% (95 % CI 72 - 91%) in adolescents, while impaired mobility affected about 61% (95% CI 48 - 72%) of adolescents. School enrolment was 53% (95% CI: 39 - 67%), with 9% (95% CI: 4% - 19%) in specialized education. Speech, hearing, and bowel dysfunction were understudied (< 2 studies each). Conclusion Many children with NTDs in the Eastern African region survive beyond infancy but frequently experience hydrocephalus, neurogenic bladder and motor impairment. Longitudinal studies, context-specific guidelines, and follow-up systems are urgently needed to improve care and long-term outcomes.