Many children deal with fatigue for which no proper treatment can be given. A possible explanation for their fatigue is a micro deficiency of minerals and vitamins. In this non-randomized controlled trial, we clinically evaluated symptoms of fatigue in children for whom a nutrient-rich diet was advised. A group of 98 children (2–18 years old) with unexplained symptoms of fatigue was examined. The dietary modifications consisted of green vegetables, beef, whole milk and full-fat butter. Children in the intervention group were asked to follow the diet for three months, whereas the control-group followed their normal diet. The primary outcome was symptoms of fatigue, as determined by a PedsQL Multidimensional Fatigue Scale, and secondary outcomes were compliance with the diet and BMI. Children, who followed the diet showed a significant decrease in the need to sleep (CI 0.83; 14.86, p = 0.03). They slept better through the night and took fewer naps. When analyzing components of the advised diet separately, a significant larger decrease in cognitive fatigue symptoms was seen for eating green vegetables according to the diet guidelines (CI 2.27; 30.63, p = 0.024). Furthermore, a lower need to sleep was seen when whole milk was consumed almost daily (CI 0.02; 14.62, p = 0.049). Our study showed that nutritional advice is an elegant, and effective method for decreasing some symptoms of medically unresolved fatigue in children.