Cognitive science principles can facilitate integrating and retaining basic science concepts during the clinical years of undergraduate medical education. We hypothesized that reinforcing foundational science concepts during the core clerkship experiences fosters the development of clinical reasoning in medical students. A patient simulation session on diabetic ketoacidosis (DKA) in the pediatric clerkship was chosen to pilot the program. We introduced an intervention in which a team of clinical and foundational science faculty facilitates student discussions, helping them connect important physiological and pathophysiological concepts to the disorder's clinical presentation, diagnosis, and management. The student survey reported that 87% strongly agreed that it helped them reinforce their understanding of foundational science concepts related to clinical cases. The National Board Medical Examination (NBME) subject exam results of the pediatric clerkships from the corresponding years were subjected to a cognitive diagnostic assessment called the DINA (deterministic input, noisy "and" gate) model analysis. The student content mastery in acid-base disorders was improved following the intervention (student mastery of skills, 0.73 vs. 0.80, P = 0.035). Similarly, analysis of the Step 2 Clinical Knowledge (CK) skills from the NBME subject exam item analysis reports showed improvement in the skill "diagnosis" on the topic of diabetes (probability value: before and after the intervention, respectively, 0.73 and 0.85, P = 0.04) following implementation. Our study shows the impact of foundational science reinforcement during clinical clerkships in developing undergraduate medical students' clinical reasoning and diagnostic skills.