(1) Background: spatial thinking is indirectly applied in numerous daily activities (e.g., when defining the route when going to school/work) or in scientific areas (e.g., predicting the spatial–temporal spread of contagious diseases), and its ability might be improved using geographical information systems (GIS). The main objective of this study was to perform an analysis of the spatial thinking of students in two curricular units (CUs) that had come from different background areas; (2) Methods: to that end, the Spatial Thinking Ability Test (STAT), composed of 15 multiple choice questions to measure spatial thinking, was given to 83 students before and after exposure to GIS concepts and software. Students’ answers were analyzed question-by-question and as total scores. The statistical analysis was performed using the paired samples t-test, the independent samples t-test or the Mann–Whitney statistical test and the nonparametric Kruskal–Wallis test; (3) Results: an overall significant improvement was observed from the pre- to the post-test. Additionally, total scores were not significantly different between students of different CUs, courses, or genders; (4) Conclusions: this exploratory study can be considered as a support methodology for pedagogical didactics that have been implemented in the CUs and may be readily applied in other academic environments, namely with students from different backgrounds, countries, and teaching strategies, thus promoting the discussion of all such experiences and consequent improvement in geographical education.