Objective: To analyze the relationship between anxiety, self-esteem, happiness index and primary school students’ academic performance in Chilean adolescents from the Biobío province. Methodology: 733 (46.1% girls; 12 (1.3 years)) public primary school students that completed the 2018 Health and School Performance Survey carried out in the Biobío province were included in this cross-sectional analysis. The BECK Anxiety Inventory (BAI) was used to measure anxiety while happiness index and self-esteem were measured using the subjective happiness scale and the Rosenberg self-esteem scale, respectively. School performance was measured by grade point average (GPA) of language, math, physical education and cumulative GPA, and behavior associated with cognition in the school context was also considered. The relationship between mental health indicators and school performance was investigated using a one-way ANOVA and Pearson correlation. Results: In comparison to students with low anxiety levels and high self-esteem and happiness levels, students with higher anxiety levels, lower self-esteem and happiness levels perceived themselves as having memory problems. They were also slower to solve math problems, had a shorter attention span in class and presented more difficulties in solving complex tasks, as well as being more nervous during testing. These students also got the lowest grade point average in math, language and physical education. Conclusions: High anxiety levels, low self-esteem and low happiness levels were associated with lower school performance and weaker behavior associated with cognition in Chilean adolescents. Implementing plans of emotional education and mental health could improve academic achievement.