Fragmented urban growth in Latin American intermediate cities has increasingly displaced low-income populations to peripheral areas, creating spatial mismatches between residential areas and educational opportunities provided by public higher education institutions. These patterns reflect inequalities that constrain educational accessibility and limit urban resilience. To examine these dynamics, this study applies a geospatial framework to develop an Educational Spatial Injustice Index (ESII) that quantifies disparities in Chihuahua, Mexico. Mobility metrics derived from Google Maps API are combined with census microdata, to analyze 108 high-demand census tracts (AGEBs) linked with seven public higher education institutions. The ESII is constructed through a multi-criteria weighting scheme based on travel time, monetary cost and network distance. Results show a clear north–south pattern, with higher ESII values concentrated in southern peripheries (0.85/1.0), where mean daily travel time reaches 3.45 h. Statistical analysis shows that the Social Lag Index (IRS; ρ = 0.729) has the strongest association with the Global ESII. Furthermore, spatial regression modeling reveals that while operational transit connectivity (bus routes) is a significant mitigating factor (p < 0.001), the mere physical presence of infrastructure (bus stops) is not. These findings suggest that spatial injustice in educational accessibility is more deeply rooted in structural urban growth patterns and socio-spatial inequalities than in simple infrastructure provision. The results support targeted planning strategies to improve accessibility and strengthen urban resilience in intermediate cities.