Despite the individual merits of Phenomenon-Based Learning (PhenoBL) and Geographic Information Systems (GIS) in improving geographic comprehension, limited research exists on their combined impact in secondary geography teaching, particularly in the Thai educational context. This study investigated the integration of PhenoBL and GIS to enhance student engagement and geo-literacy among 30 Grade 8 students in Thailand through an action research design with three iterative cycles over eight weeks. The intervention, focusing on urbanization and environmental sustainability, utilized Google Maps as a GIS tool for spatial analysis. Data collection included geo-literacy tests, student engagement surveys, and classroom observations, analyzed through paired t-tests and Pearson correlation analyses. Results demonstrated significant improvements in geo-literacy scores (from 59.5–72.5%, p < 0.01) and increases across all engagement dimensions (behavioral, emotional, and cognitive). Correlation analyses revealed a significant positive relationship between emotional engagement and geo-literacy improvement (r = 0.309, p < 0.05), while behavioral and cognitive engagement showed no significant correlations with geo-literacy gains. This suggests that emotional connection to learning activities may play a particularly important role in geographic understanding. Qualitative observations documented students’ progressive development of independence and confidence in using GIS tools. These findings provide valuable insights for educators and policymakers implementing technology-enhanced, inquiry-based learning models in geography education, while highlighting the importance of nurturing students' emotional engagement alongside structured support in GIS integration.