Background In Rwanda, cardiovascular diseases (CVDs) ranked second of the most common cause of death in 2016.  CVD risk score tools have been recommended to identify people at high risk for management. Objective To assess the comparability of body mass index (BMI)-based and lipid-based CVD risk scores in Rwandan population. Methods Secondary analysis was conducted on 4185 study participants extracted from the dataset of Rwanda 2012-2013 non-communicable diseases risk factors survey. Individual CVD risk scores were calculated using both BMI-based and lipid-based algorithms, one at a time. Spearman rank’s coefficient and Cohen’s Kappa coefficient were used to compare the two tools. Results About 63.5% of participants were women. There was a significant positive correlation between BMI-based algorithm and lipid-based algorithm vis-à-vis a 10-year CVD risk prediction (Spearman rank correlation coefficients > 0.90, p<0.001) considering either men, women or overall study participants. There was a moderate agreement between BMI-based and lipid-based algorithms vis-à-vis CVD risk characterization, kappa = 0.52; p-value p<0.001 considering either overall study participants or men and kappa = 0.48; p-value p<0.001 considering women. Conclusion The findings from this study suggest the use of BMI-based algorithm, a cost effective tool compared to lipid-based tool, can be alternatively used in resource-limited settings.  Rwanda J Med Health Sci 2021;4(1):166-184