This study aimed to investigate the effects of a 12-week high-intensity interval training on inflammatory cytokines, adipokines, and markers of bone turnover and examine whether high-intensity interval training-induced changes in inflammatory cytokines and adipokines were associated with changes in markers of bone turnover. Twenty-four women with obesity (mean [standard deviation]: age: 36.1 [3.38] years, height: 158.9 [11.9] cm, and body mass index: 31.9 [1.5] kg/m²) were randomly assigned to either control (n=10) or high-intensity interval training (n=14) groups. Body mass (− 2.7%), fat mass (− 15%), and percent body fat (− 6.2%) significantly decreased (p<0.05), while the predicted V̇O_2max increased (29.6%; p<0.001) following the high-intensity interval training program. The training program resulted in increased adiponectin (7.6%) and osteocalcin (11.3%; p<0.05) and reduced tumor necrosis factor alpha (66.1%), interleukin-1α (18.6%), C-reactive protein (24.0%), leptin (21.5%), and carboxy-terminal telopeptide cross-linking type one collagen (14%; p<0.05). When high-intensity interval training and control groups were analyzed separately, training-induced changes in inflammatory cytokines and adipokines were not associated with changes in bone turnover markers (p>0.05), whereas significant associations were found when the data of the groups were analyzed together (p<0.05). In conclusion, a 12-week high-intensity interval exercise program improves the inflammatory state, adipokines, markers of bone turnover, cardiorespiratory fitness, and body composition in women with obesity.