Skeletal muscle and adipose tissue play an important role in maintaining metabolic homeostasis and thermogenesis. We aimed to investigate the effects of single and repeated exposure to whole-body cryotherapy in volunteers with different physical fitness levels on 25-hydroxyvitamin D (25(OH)D) and myokines. The study included 22 healthy male volunteers (mean age: 21 ± 1.17 years), who underwent 10 consecutive sessions in a cryogenic chamber once daily (3 minutes, -110 °C). Blood samples were collected before and 30 minutes and 24 hours after the first and last cryotherapy sessions. Prior to treatment, body composition and physical fitness levels were measured. After 10 cryotherapy treatments, significant changes were found in myostatin concentrations in the low physical fitness level (LPhL) group. The 25(OH)D levels were increased in the high physical fitness level (HPhL) group and decreased in the LPhL group. The HPhL group had significant changes in the level of high-sensitivity interleukin-6 after the first treatment. The LPhL group had significant changes in 25(OH)D, irisin, and myostatin levels after the tenth treatment. Our data demonstrated that in healthy young men, cryotherapy affects 25(OH)D levels, but they were small and transient. The body's response to a series of 10 cryotherapy treatments is modified by physical fitness level.