Critical thinking skills and cognitive learning outcomes in Islamic primary school Science remain low, as reflected in Malaysia's below-average TIMSS 2019 performance. This study examines the effect of the Problem Based Learning model integrated with Education for Sustainable Development (PBL-ESD) on Grade VI students of Sekolah Rendah Ugama Al-Hilal, Kota Bharu, Kelantan, Malaysia. A quasi-experimental method with a Nonequivalent Pretest-Posttest Control Group Design was applied (n = 48; experimental = 30, control = 18). Data were analyzed using Shapiro-Wilk, Levene's Test, Mann-Whitney U, and N-Gain. Results revealed significant differences in cognitive learning outcomes (U = 68,000; Z = -4.332; p = .000; N-Gain: experimental = 0.742 [high], control = 0.312 [moderate]) and critical thinking (U = 82.500; Z = -3.999; p = .000; N-Gain: experimental = 0.645 [moderate], control = 0.297 [low]). Beyond categorical classification, the practical magnitude of these gains is substantial: the experimental group outperformed the control group by a mean difference of 35.56 points in cognitive learning outcomes and 31.04 points in critical thinking on the posttest, corresponding to N-Gain differentials of 0.430 and 0.348, respectively—effect sizes that exceed typical benchmarks for large practical significance in educational interventions. These findings indicate that the PBL-ESD model is pedagogically effective in improving both cognitive learning outcomes and critical thinking skills in Islamic primary school Science, with gains large enough to be readily observable in classroom practice rather than merely statistically significant.