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Rationale: The successful deployment of malaria vaccines requires not only achieving initial vaccine uptake but also ensuring completion of the recommended multi-dose schedule. However, evidence on real-world implementation performance and retention patterns of the R21/Matrix-M malaria vaccine in rural African healthcare settings remains limited. Understanding where attrition occurs across the vaccination cascade is essential for designing targeted strategies that maximize vaccine impact. Objective: This study evaluated uptake, retention, geographic variation, and implementation bottlenecks affecting completion of the four-dose R21/Matrix-M malaria vaccine schedule among children aged 5-11 months in rural Niger Delta healthcare facilities. Methods: A retrospective programme evaluation was conducted using aggregated vaccination records from nine primary healthcare facilities. The analysis assessed dose-specific coverage, facility- and community-level disparities, retention across vaccination transitions, and the relative contribution of implementation failure points. Coverage was calculated using the registered eligible catchment population (n = 4,714), while retention and dropout analyses quantified losses throughout the vaccination cascade. Results: Among 4,714 eligible children, 2,487 initiated vaccination, achieving 52.8% Dose 1 coverage. Retention declined to 72.1% after Dose 2 (1,794 children), 57.8% after Dose 3 (1,437 children), and 0.9% after Dose 4 (23 children). Facility-level Dose 1 uptake ranged from 12.8% to 87.4%, whereas no facility exceeded 2.0% booster completion. Geographic disparities were observed, with Oloibiri and Anyama clans demonstrating higher initiation coverage (75.6% and 71.2%, respectively) compared with Abureni (18.3%). The largest implementation failure occurred between Dose 3 and Dose 4, accounting for 1,414 losses (57.4% of post-initiation dropout). Conclusion: R21/Matrix-M vaccine implementation achieved moderate initial reach but experienced severe failure in maintaining children through schedule completion. The dominant programme constraint was inadequate retention rather than vaccine initiation alone. Recommendation: Malaria vaccine programmes should incorporate longitudinal tracking systems, caregiver reminder platforms, community health worker follow-up, and integration with routine immunization services to improve completion rates. These findings show that vaccine availability does not guarantee population protection; sustainable malaria control requires implementation systems that can convert early vaccine access into complete vaccination coverage.