Historically in developing countries, the prevalence of obesity has been greater in more advantaged socioeconomic groups. However, in recent years the association between socioeconomic status (SES) and obesity has changed and varies depending on the country's development stage. This study examines the relationship between SES and obesity using two indicators of SES: education or possession assets. Using the cross-sectional 2008 National Demographic and Family Health Survey of Peru (ENDES 2008), we investigated this relationship in women aged 15–49 years living in rural and urban settings. Descriptive, linear and logistic regressions analyses were conducted accounting for the multistage nature of the sampling design. The overall prevalence of obesity in this study was 14.1% (95% confidence interval (CI): 13.3–14.8); 8.4% (95% CI: 7.5–9.3) in rural areas and 16.2% (95% CI: 15.2–17.2) in urban areas. Wealthier women were more likely to be obese, and this association was stronger in rural areas. Conversely, more educated women were less likely to be obese, especially in urban areas. The distribution of obesity in Peruvian women is strongly related to socioeconomic position, and differs whether measured as possession assets or by level of education. These findings could have important implications for policy development in Peru.