This study was conducted to determine the prevalence of calcium and vitamin D deficiency in school children aged 6 to 11 years in Lviv (Ukraine). The aim of this study was also to assess the effect of nutritional intervention and supplementation on serum calcium and vitamin D levels in children diagnosed with calcium deficiency. A 3 day diet was analyzed in 172 children. In 56 children with a deficiency of calcium and/or vitamin D, the level of total calcium, ionized calcium, and 25-hydroxyvitamin D in blood, as well as the calcium content in hair samples, was determined. Thirty children with confirmed calcium and/or vitamin D deficiency underwent a dietary intervention to increase calcium and vitamin D intake for 3 months. The study group (n = 15) was provided with a nutritional correction by modifying their diet with supplementation of calcium and vitamin D. The control group (n = 15) received only a diet modification. Decreased daily calcium intake was observed in 50.68% of boys and 70.71% of girls. A decreased level of daily vitamin D consumption was found in 84.93% of boys and 96.97% of girls. Among 56 children with insufficient daily consumption of calcium and/or vitamin D, 26.8% had reduced levels of total calcium in the blood, 16.1% had reduced levels of ionized calcium in the blood, and 48.2% had reduced levels of vitamin D. After 3 months of correction, normal calcium level was found in the hair of 10 students (66.7%) from the study group and in three subjects (20.0%) from the control group. Modification of the diet along with supplementation of calcium and vitamin D seems to be a more effective method for increasing the level of calcium among children aged 6 to 11 years.