Background This study aims to compare the differences in the means of bone formation and resorption markers between young adult male smokers and nonsmokers. Methods This study employed a cross-sectional, descriptive design. Thirty-five smokers and 38 nonsmokers were recruited. All participants completed self-reported questionnaires about demographics, physical activity, and smoking status. In addition, blood specimens were collected to determine serum levels of bone turnover markers. Results Regarding bone formation markers, the least square means (LSM) for osteoprotegerin (OPG) and procollagen type I N-terminal propeptide (PINP) were similar for smoking and nonsmoking groups. Regarding bone resorption markers, the LSM serum carboxyl-terminal telopeptide of collagen type I (CTXI) level was found to be significantly lower in smokers than nonsmokers [0.82 ± 0.83 vs. 1.30 ± 0.82 ng/mL, F (1, 66) = 5.73, p = 0.020]. The LSM for soluble-receptor activator of nuclear factor-kappa B ligand (sRANKL) [1.64 ± 0.60 vs. 1.69 ± 0.62 ng/mL, F (1,64) = 10.74, p = 0.002] and RANKL/OPG [2.62 ± 1.09 vs. 2.81 ± 1.10 ng/mL, F (1,65) = 5.88, p = 0.018] were different for smoking and nonsmoking groups. Exploration of the moderating influence of physical activity on smoking effects revealed significant effect for the interaction between smoking status and physical activity on sRANKL [F (2, 64) = 8.63, p = 0.001] and RANKL/OPG ratio [F (2, 65) = 5.49, p = 0.006]. Conclusion Our study provides evidence for the effect of smoking on bone resorption markers in young adult males. Such effects should be carefully considered side by side with other lifestyles that may lead to poor bone health and increased risk for osteoporosis.