Mexican migrant farm workers are one of the poorest and most marginalized social groups within the country. They face the double burden of malnutrition, food insecurity, as well as harsh living and labor conditions. Objective: To examine the relationship between household food insecurity (HFI) and obesity in a population of migrant farm workers in highly modernized agribusiness areas of Northwest Mexico. Methods: This was a cross-sectional study with a concentric (site) (n = 146 households) and systematic selection of participants (adult men and women). Methods included questionnaires regarding socio-demographic characteristics, food security, diet (two non-consecutive 24-h recalls), and physical activity (PA). Anthropometric data included height, weight, and waist circumference. Data analysis covered descriptive statistics, multivariate linear and logistic regression. Results: Sample showed 75% prevalence of overweight and obesity, while 87% of households reported some level of HFI. Mild HFI resulted in five times more probability of farm workers’ obesity (OR = 5.18, 95% CI: 1.37–19.58). However, there was a protective effect of HFI for obesity among men (OR 0.089, 95% CI: 0.01–0.58) in a context of intense labor-related PA. Conclusion: There is a difference by gender in the relationship of HFI with obesity prevalence related perhaps to the energy expenditure of male agricultural migrant workers.