Nutritional status of children with chronic kidney disease (CKD) is important since it affects growth and development. This study was to investigate overall diet quality measured by nutrient intake adequacy, nutrient density, and several dietary habits in children with CKD and its relationship with clinical parameters according to glomerular filtration rate (GFR). Assessment of nutritional status and diet quality was conducted in nineteen children with CKD. Average Z-scores of height, weight and body mass index (BMI) in the participants were less than standard growth rate. Nutritional status, such as Z-scores of height (p < 0.05) and serum total protein (p < 0.05), were significantly lower in the children with GFR < 75 mL/min/1.73 m² compared to those with GFR ≥ 75 mL/min/1.73 m². Nutrition adequacy ratio of energy, thiamin, riboflavin, vitamin B₆, folate, iron, and zinc and overall diet quality were significantly poorer in the children with GFR < 75 mL/min/1.73 m². Poorer appetite and avoidance of food were observed in the children with higher blood urea nitrogen (BUN). Intakes of iron, zinc, thiamin, niacin, and vitamin B₆ were positively correlated with GFR. Intakes of calcium, potassium and folate were positively correlated with BUN, while protein intakes were negatively correlated. Overall nutrient intakes were inadequate and diet quality was decreased as kidney function was decreased. Dietary habit and appetite were also related with kidney function in this study subjects. Systemic efforts of nutritional intervention are imperative to prevent deteriorating growth and development and improve the nutritional status in children with CKD.