Although numerous studies have approached the effects of exposure to a Western diet (WD) on academic outcomes, very few have focused on foods consumed during snack times. We explored whether there is a link between nutritious snacking habits and academic achievement in high school (HS) students from Santiago, Chile. We conducted a cross-sectional study with 678 adolescents. The nutritional quality of snacks consumed by 16-year-old was assessed using a validated food frequency questionnaire. The academic outcomes measured were HS grade point average (GPA), the likelihood of HS completion, and the likelihood of taking college entrance exams. A multivariate analysis was performed to determine the independent associations of nutritious snacking with having completed HS and having taken college entrance exams. An analysis of covariance (ANCOVA) estimated the differences in GPA by the quality of snacks. Compared to students with healthy in-home snacking behaviors, adolescents having unhealthy in-home snacks had significantly lower GPAs (M difference: -40.1 points, 95% confidence interval (CI): -59.2, -16.9, d = 0.41), significantly lower odds of HS completion (adjusted odds ratio (aOR): 0.47; 95% CI: 0.25-0.88), and significantly lower odds of taking college entrance exams (aOR: 0.53; 95% CI: 0.31-0.88). Unhealthy at-school snacking showed similar associations with the outcome variables. Poor nutritional quality snacking at school and at home was associated with poor secondary school academic achievement and the intention to enroll in higher education.