Background: Anthropometric indices such as body mass index (BMI) is a widely used index of adiposity across clinical settings, yet there are limitations regarding their estimates of body fat. We determined the magnitude and the performance of fat mass index (FMI), and percentage body fat (PBF) for determining obesity among undergraduate students in the Kumasi Metropolis, Ghana. Methods: This University community-based cross-sectional study included 1,552 undergraduate students (700 males and 852 females) aged 15–29 years from the Kwame Nkrumah University of Science and Technology, Kumasi, Ghana. Anthropometric measurements and bioelectrical impedance analyses were performed. Data on sociodemographic and lifestyle-related characteristics were obtained using a structured questionnaire. Results: Comparing male to female students, the age-standardised prevalence of overweight/obesity was 10.8%/3.5% vs. 19.3%/7.6% (p<0.0001) for BMI criterion, 16.4%/8.5% vs. 21.9%/19.9% (p<0.0001) for PBF criterion and 16.0%/9.2 vs. 21.2%/22.0% for FMI criterion (p<0.0001), respectively. There was a stronger agreement between PBF and FMI in the classification of overweight and obesity in terms of males (kappa=0.855) and females (kappa=0.865) but a weak agreement between BMI and PBF and between BMI and FMI. About 29.3% of males and 61.4% of the females categorized as normal weight by BMI were identified as overweight by PBF. Similarly, 3.0% of male and 1.3% of females defined as normal weight by BMI were obese when examined by PBF. FMI can be predicted from BMI and BMI2 with much accuracy (mean bias = -0.1). Conclusion: The inconsistency observed between BMI and PBF reflects a limitation of BMI. FMI accurately assessed obesity with many conveniences as BMI to the same extent.