This study determined the effect of the Cuisenaire Rods app on Grade 6 learners’ performance in dissimilar fractions at Catigbian Central Elementary School, Poblacion, Catigbian, Bohol, during the school year 2025–2026. An explanatory sequential mixed-methods design was used. The quantitative phase involved 45 Grade 6 learners in a one-group pretest–posttest design, while the qualitative phase involved one-on-one interviews with 10 selected participants. A researcher-made proficiency test measured four competencies: simplifying fractions, identifying equivalent fractions, adding dissimilar fractions, and subtracting dissimilar fractions. Results showed that the overall mean score increased from 71 in the pretest to 77 in the posttest. The proportion of learners at the Advanced level increased from 2% to 20%. Significant differences were found between pretest and posttest scores in simplifying fractions (t = -8.21, p = 0.0019), identifying equivalency (t = -8.22, p = 0.001), adding dissimilar fractions (t = -7.20, p = 0.004), and subtracting dissimilar fractions (t = -7.70, p = 0.009). Qualitative findings revealed three advantages of the app: improved understanding of fractions, development of skills and personal growth, and increased motivation and engagement in learning. Reported challenges included visual clarity and focus issues, and a lack of mastery in using the app due to technical responsiveness concerns. The study concludes that the Cuisenaire Rods app is a promising supplementary tool for teaching dissimilar fractions, although sustained exposure, teacher guidance, and technical support remain necessary.