Background: The impact that dietary carbohydrates have on children developing type 2 diabetes remains controversial. Furthermore, there are limited pediatric longitudinal studies on changes in body mass index (BMI) and diet related to the development of acanthosis nigricans (AN), a risk factor associated with type 2 diabetes. Methods: Two 24 h dietary records were collected for 558 children, 2–8 years of age, at baseline and at a 2-year follow-up. Data on age, sex, BMI, and the presence of AN were also collected at each time point from the Children’s Healthy Living Program. Logistic regression was used to determine factors associated with the presence of AN at follow-up. Multinominal regression was used to determine factors associated with changes in AN status. Linear regression was used to measure the associations between changes in dietary intake and in the Burke Score for AN. Results: AN was present in 28 children at baseline and 34 children at follow-up. Adjusting for the presence of AN at baseline, age, sex, study group, baseline BMI, change in BMI z-score, time between assessments, and baseline intake, an increase from baseline for each teaspoon of sugar and serving of carbohydrate-rich food increased the risk for having AN at follow-up by 9% and 8%, respectively (p≤ 0.05). An increased intake of added sugar (teaspoons) increased the risk of developing AN by 13% (p≤ 0.01) and an increase in servings of foods rich in starch increased the risk of developing AN by 12% (p≤ 0.01) compared to children who never had AN. Increasing the intake of fruit was also associated with decreased Burke Scores using multiple regression. However, the intake of energy and macronutrients were not associated with AN. Conclusions: Added sugar and foods rich in starch were independently associated with the occurrence of AN, suggesting the type of carbohydrates consumed is a factor in AN occurrence.