This study investigated the impact of Geographic Information Systems (GIS) integration on secondary-level pupils' spatial thinking and geographic concept comprehension in urban schools of Zambia's Eastern Province. Employing a concurrent mixed-methods design, 150 pupils from GIS-exposed and non-exposed groups completed validated spatial reasoning instruments — the Mental Rotation Test (MRT) and the Perspective Taking/Spatial Orientation Test (PTSOT) — while ten geography teachers participated in in-depth semi-structured interviews. Quantitative analyses revealed statistically significant and practically large differences in favour of GIS-exposed pupils across all three cognitive measures (p < 0.001), with effect sizes ranging from Cohen's d = 0.93 to d = 1.49. A multiple regression model identified lesson frequency (β = 0.51) and teacher Technological Pedagogical Content Knowledge (TPACK) (β = 0.36) as significant predictors of spatial visualisation, collectively explaining 45% of the variance (R² = 0.45). Qualitative thematic analysis of teacher interviews surfaced four dominant themes: infrastructure constraints, professional development deficits, pedagogical adaptations, and enhanced student engagement. Despite widespread power outages and limited connectivity, all ten teachers successfully employed scaffolded instructional strategies and peer-collaboration models to sustain GIS-based learning. The findings affirm GIS's transformative potential for spatially literate geography education in resource-constrained African contexts and provide evidence-based recommendations for curriculum policy, teacher training, and infrastructure investment.