Mental health problems, including emotional problems, are linked to adverse educational outcomes among children and adolescents. This study examines the association between early onset of mental health problems generally, and emotional problems specifically, at ages 5-14, and outcomes from the General Certificate of Secondary Education (GCSE), a secondary education qualification, at age 16 for 4,783 students in England, using the Millennium Cohort Study dataset linked to the National Pupil Database. We found that the onset of mental health problems at ages 5, 7, 11 and 14 had a significant and negative association with all GCSE outcomes. We also found negative associations between early onset emotional problems and GCSE outcomes, although results were most stark for emotional problems that onset at age 11, with statistically significant negative associations with all GCSE outcomes. School absence was identified as a potential mediator of the negative association. Furthermore, this study found that the potential loss of productivity related to mental health problems in general and emotional problems in particular was over 23,000 sterling and 11,000 sterling per affected individual, respectively, which could translate into approximately 2.57 billion sterling and 1.6 billion sterling, respectively at the population level for England. These findings highlight the importance of early intervention for children and adolescents with mental health problems to improve educational and future outcomes.