Vitamin D deficiency that remains non-compensated for a long time is associated with high risk of rickets in children and osteomalacia in adults, myopathies and low-energy fractures, as well as secondary hyperparathyroidism (SHPT). SHPT represents one of the main mechanisms, through which vitamin D deficiency can contribute to pathogenesis of low-energy fractures. The study was aimed to assess the calcium and phosphorus metabolism state and the bone tissue metabolism markers in highly trained athletes with SHPT, as well as the prevalence of SHPT in elite sports. The study involved 527 young athletes aged 12–18 years (average age 15.2 years) doing 32 sports. The group with SHPT included 16 children (11 girls and 5 boys) with the average age of 15.0 years. The control group with normal levels of parathyroid hormone consisted of 511 children (254 boys and 273 girls) with the average age of 15.2 years. The studied subgroups were matched by age (p = 0.678). Girls predominated in the group with SHPT (р = 0.02). SHPT associated with vitamin D deficiency was revealed in 3% of young highly trained athletes, it was more prevalent among girls. The SHPT development does not result in alteration of the calcium and phosphorus metabolism indicators, however, it is accompanied by the increase in bone resorption markers, β-CrossLaps and total alkaline phosphatase. Many aspects related to vitamin D deficiency in SHPT are currently poorly understood, and there are no clinical guidelines on the cholecalciferol replacement therapy. Large-scale clinical trials are required to determine the optimal threshold values of 25(ОН)D3 and the powerful and effective treatment regimens for young athletes having SHPT associated with vitamin D deficiency.