The study aimed to investigate students' psychological, cognitive, and social well-being in 6th Grade and the relations to academic achievement in compulsory school, as measured by grades in 9th Grade. Due to reports from Swedish authorities and research, students' self-reported well-being has decreased during the last decade. Data from the Swedish longitudinal project Evaluation Through Follow-up was analyzed with confirmatory factor analysis and structural equation modelling. By using data from two birth cohorts (1998: N = 7 684 and 2004: N = 9 437), differences in well-being across the two cohorts could be investigated. Cognitive ability, parental education, and gender were also accounted for. Statistically significant cohort and gender differences were found, where cohort 2004 was disadvantaged in all three well-being dimensions, and girls were disadvantaged in psychological and social well-being. Psychological well-being was negatively related to academic achievement, indicating that students who experienced more school-related stress performed higher than students who experienced less stress. Cognitive well-being was positively related to academic achievement. Possible causes of the decrease in well-being may be changes in the educational and assessment system, which meant that cohort 2004 went through compulsory school with a stronger focus on results and grades than earlier cohorts.