Background: Poor diet quality in children and adolescents may contribute to decreased immunity and lead to an increased risk of opportunistic diseases. Aim: To investigate diet quality and its relationship to nutritional status in human immunodeficiency virus (HIV)-infected pediatric patients (HIV-PIHIV). Methods: We conducted a cross-sectional study with 87 patients aged between 6 and 19 years carried out in two University Hospitals. Diet quality was analyzed by an adapted Healthy Eating Index (HEI) and nutritional status. The association between HEI with body mass index-for-age (BMI-for-age) and height-for-age was performed using a linear regression model. Clinical, maternal, anthropometric, and dietary data were collected through a semi-structured questionnaire, based on nutrition service protocols. Results: Diet quality was intermediate (median IAS = 54.8 interquartile range: 47.5 to 65.9 points), due to low consumption of fruits, vegetables, and dairy products and high empty calories and sodium by the PPIHIV. The multivariate regression model indicated that HEI was not significant for explaining BMI-for-age [β = −0.01; 95% CI = (−0.03; 0.01); p 0.40] nor height-for-age [β = 0.01; 95% CI = (−0.02; 0.03); p 0.51]. However, it was observed that adolescents showed 1 Z-score [95% CI = (−1.6; −0.44); p 0.001] a reduction in BMI-for-age compared with children, and those black patients showed an increase in BMI-for-age Z-score of 0.57 [95% CI = (0.7; 1.1); p 0.03] compared with non-blacks. Conclusion: The diet quality of the HIV-infected children and adolescents was below desired. No association was found between diet quality and inadequate nutritional status of HIV-PIHIV.