Research integrating GeoGebra with the Anthropological Theory of the Didactic (ATD) remains limited, particularly regarding how dynamic visualisation within a structured praxeological framework influences students’ critical thinking. This study examined the effectiveness of a GeoGebra-assisted learning sequence structured around four praxeological components: task, technique, technology, and theory. A quasi-experimental non-equivalent control group design involved 63 second-semester Differential Calculus students at STKIP Taman Siswa Bima, Indonesia, comprising 32 experimental and 31 control participants. Both groups received instruction from the same lecturer across eight 100-minute sessions. Critical thinking was assessed using a ten-item essay test covering interpretation, analysis, evaluation, inference, and explanation, with satisfactory content validity (0.89) and reliability (Cronbach’s α = 0.84). Pre-test scores showed no significant difference between groups (p = 0.784). Following the intervention, the experimental group significantly outperformed the control group (t(61) = 5.274, p < 0.001), with a mean difference of 11.53 (95% CI: 7.16–15.90) and a large effect size (Cohen’s d = 1.33). Normalised learning gains were moderate in the experimental group (0.53) and low in the control group (0.28). Significant improvements were observed across all five critical thinking dimensions, although explanation remained the weakest. These findings suggest that integrating GeoGebra with ATD-based praxeological organisation strengthens critical thinking by connecting dynamic visual exploration with mathematical justification and generalisation. The proposed instructional framework offers a practical approach to improving undergraduate calculus learning.