In recent years, there has been increasing interest in the homeostatic response to extreme exercises, especially in the integrated function of muscle and bone. The aim of this study was to evaluate the effects of a marathon race on selected myokines and sclerostin in 10 male recreational runners (mean age 41 ± 7.7 years). Body composition, bone mineral density (BMD), and the serum concentration of myostatin, irisin, sclerostin, osteoprotegerin (OPG), 25-hydroxyvitamin D (25(OH)D), parathyroid hormone (PTH), high-sensitivity interleukin-6 (hsIL-6), tumor necrosis factor α (TNFα), high-sensitivity C-reactive protein (hsCRP) and myoglobin, were determined 24 h before and 24 h and 72 h after a marathon race. Post-marathon increases were observed in the levels of myostatin (1.2-fold), OPG (1.5-fold), and PTH (1.3-fold), hsIL-6 (1.9-fold), myoglobin (4.1-fold), hsCRP (fivefold), TNFα (2.6-fold), after 24 h; and in myostatin (1.2-fold), irisin (1.1-fold), sclerostin (1.3-fold), OPG (1.3-fold), and PTH (1.4-fold), hsIL-6 (1.4-fold), TNFα (1.9-fold), after 72 h compared to the baseline level. The results show that in response to the marathon run, a complex network of endocrine interactions is initiated. Further research is needed to fully elucidate the long-term impact of prolonged high intensity exercise on the human body.