This three-phase prospective study investigated psychosocial factors predicting or associated with academic achievement. An initial sample of 1,514 school-age children was assessed with screening tools for emotional problems (Screen for Childhood Anxiety and Related Emotional Disorders; Leyton Obsessional Inventory-Child Version; Children’s Depression Inventory). The following year, 562 subjects (risk group/without risk group) were re-assessed and attention deficit/hyperactivity disorder (ADHD) was assessed. Two years later, 242 subjects were followed, and their parents informed about their academic achievement. Results showed that early depression (phase 1 B = –.130, p = .001; phase 1 + phase 2 B = –.187, p < .001), persistent anxiety symptoms (phase 1 + phase 2 B = –1.721, p = .018), and ADHD were predictors of lower academic achievement (phase 1 + phase 2 B = -3.415, p = .005). However, some anxiety symptoms can improve academic achievement (Social phobia B = .216, p = .018; Generalized anxiety B = .313, p < .001). Socio-economic status (SES) was positively related to academic achievement. We can conclude that in the transition period to adolescence, school-health professionals and teachers need to consider the emotional issues of students to avoid unwanted academic outcomes.