This study aimed to investigate the association between social jetlag (SJL) and obesity-related outcomes among adolescents from Valle de Ricote (Region of Murcia, Spain). We explored the relationship between SJL and body mass index (BMI) z-score, waist circumference, and body fat percentage, as well as the odds of having excess weight, obesity, and abdominal obesity in a sample of Spanish adolescents. A cross-sectional study was conducted using data from the Eating Healthy and Daily Life Activities (EHDLA) project, which included 847 Spanish adolescents aged 12-17 years. SJL was assessed based on the differences in sleep patterns between weekdays and weekends. Obesity-related indicators such as BMI z-score, waist circumference, body fat percentage, excess weight, obesity, and abdominal obesity were measured. Generalized linear models with a Gaussian or binomial distribution were used to analyze the associations between SJL and obesity-related outcomes, adjusting for potential confounders. The analysis revealed significant associations between SJL and BMI z-score (unstandardized beta coefficient [B] = 0.15, 95% CI: 0.05 to 0.25, p = 0.003), waist circumference (B = 1.03, 95% CI: 0.39 to 1.67, p = 0.002), and body fat percentage (B = 0.83, 95% CI: 0.31 to 1.43, p = 0.008). Additionally, the odds ratios (ORs) for excess weight (OR = 1.35, 95% CI: 1.16 to 1.57; p < 0.001), obesity (OR = 1.59, 95% CI: 1.26 to 2.00; p < 0.001), and abdominal obesity (OR = 1.46, 95% CI: 1.23 to 1.72; p < 0.001) increased significantly with each 60 min increment in SJL. This study pointed out that the misalignment of sleeping times during weekdays and weekends (SJL) is significantly associated with higher BMI z-scores, waist circumference, body fat percentage, and higher odds of excess weight, obesity, and abdominal obesity among adolescents, being more significant in boys than in girls. These findings highlight the importance of addressing circadian misalignment in the prevention and management of obesity and its related metabolic disorders in this population.