Energy and micronutrient deficiency remain prevalent among Filipino children. Juice drinks are commonly consumed and could be a viable vehicle for fortification to supplement the nutrient gap. This study determined the effects of a newly developed non-carbonated fortified juice drink on the iron, zinc and nutritional status of schoolchildren. One hundred randomly selected anemic children were randomly allocated into two groups in a doubly-masked placebo controlled manner: Group 1 received the fortified juice, Group 2 received the non-fortified juice for 100 days, five days a week under strict supervision. The juice drink was fortified with vitamin A, zinc, iron, vitamin C and lysine. The non-fortified juice was fortified only with vitamin C. All children were dewormed prior to the intervention. Hemoglobin, plasma ferritin and plasma zinc, weight and height were assessed using standard methods before and after intervention. A two-day 24-hour food recall was also collected. The basal prevalence of anemia was significantly reduced in both the fortified group (100% to 13%) and the non-fortified group (100% to 40%) at endline. The mean plasma ferritin levels were similar in both groups at baseline and endline. At endline, mean plasma zinc in the fortified group has significantly increased by 20 μg/dL from a baseline value of 83.9 μg/dL to 103.9 μg/dL, while the non-fortified group remained at similar levels with baseline. Basal weight and height significantly increased among all children at endline. The fortified juice drink was effective in reducing the prevalence of anemia and improved the zinc status of children.