Background: Zinc is an essential micronutrient for human beings and its deficiency affects their normal growth and development. Objective: The main aim was to evaluate the effect of two doses of zinc supplementation (ZS) on the nutritional status in chronic kidney disease (CKD) children. Methods: A randomized-trial multicentric study was conducted in 48 CKD (23 females) patients under 18-years-old, for a year. At random, participants took 30 or 15 mg/day of ZS, respectively. Anthropometric measurements and biochemical analysis were performed. Hypozincemia was determined by serum zinc concentration (SZC) using atomic absorption spectrophotometry. The positive or negative change in patients’ body mass index (BMI) Z-score, serum albumin, zinc and C-reactive protein (CRP) levels were used to evaluate the effect of ZS. Results: Mean SZC was normal before and after ZS. Despite ZS, there were no significant changes in serum albumin, zinc and CRP levels. A positive and significant association was observed between SZC and serum albumin before (p = 0.000) and after (p = 0.007) ZS. In both groups of ZS, there was a small but positive and significant change in body mass and normalization in BMI Z-score, hypoalbuminemia, hypozincemia and high CRP, especially with 30 mg/day of ZS. Conclusions: Zinc supplementation may be beneficial for nutritional status in children and adolescents with CKD.