(1) Background: Childhood immunization is vital for preventing morbidities and mortalities globally. However, rural Pakistan is facing persistent challenges, particularly after recent global health crises in gauging accurate vaccination coverage estimates. This study aimed to apply a novel Lot Quality Assurance Sampling (LQAS) methodology due to its rapid and reliable estimates of the routine immunization rates among children aged 12-23 months old in Shikarpur, Sindh, and to identify priority areas for future interventions. (2) Methods: A cross-sectional household survey design was adopted for an in-depth assessment of vaccination coverage in a previously under-studied rural context. (3) Results: Data were collected from 1,402 children aged 12-23 months across 47/49 Union Councils in Shikarpur within 141 randomly identified clusters. LQAS was innovatively employed along with GIS Mapping which provided a spatial analysis of the distribution of immunization coverage and the spot map of clusters. The weighted average for fully immunized children was 42.4% after applying Direct Adjustment Method. A steep decline in coverage for each successive vaccine dose was observed, and 39 key priority areas were identified on GIS-based plotting for intensive health interventions. Multivariate Logistic Regression Model further revealed informational gaps and fear of side effects as major barriers to achieving complete immunization. (4) Conclusions: The innovative application of LQAS and GIS Mapping in this study has provided a comprehensive glimpse of its utility in future follow-ups and similar assessments. The findings stress the critical need to tackle the foundational reasons behind the vaccination gaps, with a special focus on enhancing awareness and information dissemination in the key priority areas.