Background: Many emotional and behavioral problems first emerge in primary school and are the forerunners of mental health problems occurring in adolescence. However, the extent that these problems may be associated with academic failure has been explored less. We aimed to quantify the association between emotional and behavioral problems with academic performance. Methods: A stratified random sample of 8- to 9-year-olds (N = 1239) were recruited from schools in Australia. Data linkage was performed with a national assessment of academic performance to assess reading and numeracy. Parent report assessed emotional and behavioral problems with students dichotomized into "borderline/abnormal" and "normal" categories. Results: One in 5 grade 3 students fell in the "borderline/abnormal" category. Boys with total difficulties (ß = -47.8, 95% CI: -62.8 to -32.8), conduct problems, and peer problems scored lower on reading. Numeracy scores were lower in boys with total difficulties (ß = -37.7, 95% CI: -53.9 to -21.5) and emotional symptoms. Children with hyperactivity/inattention scored lower in numeracy. Girls with peer problems scored lower in numeracy. Conclusions: Boys with emotional and behavioral problems in mid-primary school were 12 months behind their peers. Children with emotional and behavioral problems are at high risk for academic failure, and this risk is evident in mid-primary school.