Background: An unhealthy body weight is an adverse effect of malnutrition associated with morbidity among women of childbearing age. While there is increasing attention being paid to the body weights of children and adolescents in Nigeria and South Africa, a major surge of unhealthy body weight in women has received less attention in both countries despite its predominance. The purpose of this study was to explore the prevalence of body weights (underweight, normal, overweight, and obese) and individual-level factors among women of childbearing age by urban–rural variations in Nigeria and South Africa. Methods: This study used the 2018 Nigeria Demographic Health Survey data (n = 41,821) and 2016 South Africa Demographic Health Survey (n = 8514). Bivariate, multilevel, and intracluster correlation coefficient analyses were used to determine individual-level factors associated with body weights across urban–rural variations. Results: The prevalence of being overweight or obese among women was 28.2% and 44.9%, respectively, in South Africa and 20.2% and 11.4% in Nigeria. A majority, 6.8%, of underweight women were rural residents in Nigeria compared to 0.8% in South Africa. The odds of being underweight were higher among women in Nigeria who were unemployed, with regional differences and according to breastfeeding status, while higher odds of being underweight were found among women from poorer households, with differences between provinces and according to cigarette smoking status in South Africa. On the other hand, significant odds of being overweight or obese among women in both Nigeria and South Africa were associated with increasing age, higher education, higher wealth index, weight above average, and traditional/modern contraceptive use. Unhealthy body weights were higher among women in clustering areas in Nigeria who were underweight (intracluster correlation coefficient (ICC = 0.0127), overweight (ICC = 0.0289), and obese (ICC = 0.1040). Similarly, women of childbearing age in clustering areas in South Africa had a lower risk of experiencing underweight (ICC = 0.0102), overweight (ICC = 0.0127), and obesity (ICC = 0.0819). Conclusions: These findings offer a deeper understanding of the close connection between body weights variations and individual factors. Addressing unhealthy body weights among women of childbearing age in Nigeria and South Africa is important in preventing disease burdens associated with body weights in promoting Sustainable Development Goal 3. Strategies for developing preventive sensitization interventions are imperative to extend the perspectives of the clustering effect of body weights on a country level when establishing social and behavioral modifications for body weight concerns in both countries.