Background <p>Concept mapping is an active learning strategy that may promote meaningful learning and higher-order cognitive development. This study aimed to evaluate the effect of concept mapping-based instruction on Bloom’s cognitive levels and academic motivation among undergraduate public health students.</p> Methods <p>This one-group pretest-posttest quasi-experimental study was conducted among 62 undergraduate students at Kerman University of Medical Sciences, Iran, in 2025. Educational content in Lessons was delivered using concept mapping over 15 weeks. Bloom’s cognitive domains and academic motivation were assessed using researcher-developed questionnaire. Paired t-test and Pearson’s correlation were used for analysis.</p> Results <p>Significant positive correlations were observed between all Bloom’s domains and academic motivation (<i>P</i> &lt; 0.001). Following the intervention, significant improvements were found in Knowledge (<i>P</i> = 0.005), Comprehension (<i>P</i> &lt; 0.001), Analysis (<i>P</i> = 0.008), Synthesis (<i>P</i> = 0.001), Evaluation (<i>P</i> &lt; 0.001), and Academic Motivation (<i>P</i> = 0.042). However, the Application domain did not show a significant increase (<i>P</i> = 0.077).</p> Conclusion <p>Concept mapping-based instruction significantly enhanced multiple Bloom’s cognitive levels and academic motivation among public health students. The lack of improvement in the application domain suggests that developing practical skills may require complementary strategies. Further controlled studies are needed to confirm these preliminary findings.</p>