A cluster of factors affects nutritional status among adolescent girls in low- and middle-income countries (LMICs). We investigated the association between school attendance and diet quality among 498 rural adolescent girls (352 attending and 146 not attending school) in Tecpán, Guatemala. In a cross-sectional study, we collected sociodemographic and anthropometric data and characterized the dietary intake using a Food Frequency Questionnaire. We then calculated diet quality using the Healthy Eating Score (HES). Multiple linear regression models were conducted to evaluate the effects of school attendance on diet quality. We found that the overall diet quality among the study participants was poor, according to the HES. However, those who attended school had significantly higher intakes of vitamin A-rich fruits and vegetables (P = 0.04), other fruits (P = 0.01), and milk and milk products (P = 0.004), but a higher intake of fast foods, chips, and saturated fatty acids (P < 0.001). Furthermore, the effects of school attendance on diet quality were significant after adjusting for sociodemographic and lifestyle factors (β coefficient = -1.70, 95% CI: -3.30 to -0.11) but was attenuated when further adjusted for weight status (β coefficient = -1.58, 95% CI: -3.17 to 0.02). Our findings suggest that diet quality among girls in rural Guatemala is poor, particularly among those who do not attend school. To advance our understanding of adolescent diet in LMICs, future studies should include adolescents who are out of school.