Objective: To determine if there was any significant difference in scores of students who acquired knowledge through team-based learning (TBL) versus those who learned through small group discussion (SGD). Study Design: Quasi-experimental cross-over study. Place and Duration of Study: Shifa College of Medicine, Islamabad, from March to December 2015. Methodology: All students of second year MBBS were assigned to either TBL or SGD, based on non-probability sampling, for 8 themes in a five-week module. The groups were flipped after 4 themes. TBL format recommended by the AMEE guide No: 65 was followed. The impact of both learning methods was assessed by comparing end-of-module written examination scores of the two groups through independent sample t-test. SPSS version 23 was used for data analysis. A p-value of <0.05 was considered statistically significant. Results: End-of-module written examination scores showed there was no significant difference in student academic performance when they studied with TBL or SGD in themes 1-4 (TBL 61.90 ±13.01 versus SGD 59.65 ±11.56, p=0.41). However, for themes 5-8 there was a significant difference in scores (TBL 65.36 ±11.62 versus SGD 59.92 ±10.65, p=0.03) A trend towards higher scores was observed in content learned with TBL in all eight themes. Conclusion: TBL is equally effective as an instructional method as SGD. However, it could not be established that it results in significant improvement in learning.