This study explored the association between social jetlag and academic performance among adolescents in Spain, a country with structural circadian misalignment. This cross-sectional study analyzed data from 788 adolescents (55% female, 12-17 years) from the Eating Healthy and Daily Life Activities (EHDLA) study in the Valle de Ricote, Spain. Social jetlag was calculated as the absolute difference between usual weekend and weekday bedtimes (primary exposure), derived from self-reported school and weekend sleep/wake times. Academic performance was assessed via official school records: grade point average (GPA) and individual grades in language, math, foreign language, and a Programme for International Assessment (PISA) type composite score (mean of language, maths, and science grades; not the OECD PISA test). Ordinal regression models, with social jetlag as both a continuous and categorical variable, were adjusted for key confounders including age, sex, socioeconomic status, body mass index, and overall sleep duration. Each 1-h increase in social jetlag was associated with lower odds of achieving higher GPA (odds ratio [OR] = 0.76; 95% confidence intervals [CI] 0.68-0.85), language (OR = 0.80; 95% CI 0.71-0.90), maths (OR = 0.81; 95% CI 0.72-0.91), foreign language (OR = 0.75; 95% CI 0.67-0.85), and PISA-type composite (OR = 0.76; 95% CI 0.66-0.88) grades (all p < 0.01). When categorized, only severe social jetlag (> 2 h) was consistently linked to poorer academic performance across all assessed outcomes, compared to those with no social jetlag (< 1 h).