Background: In adult studies, obese subjects with nonalcoholic fatty liver disease (NAFLD) have been shown to have poor sperm quality, and lower testosterone and luteinizing hormone levels. The aim of this study was to investigate the pubertal status and gonadal functions in obese boys with NAFLD. Materials and Methods: The study included 119 obese and 78 nonobese age-matched adolescents. The obese boys were separated into two groups based on the presence (NAFLD group) or absence of liver steatosis with high transaminases (non-NAFLD group). The levels of serum AMH (anti-Mullerian hormone), inhibin B, gonadotropins, total testosterone, lipids, high-sensitivity C-reactive protein, fasting glucose, insulin levels, and aortic intima media thickness were measured in all subjects. Results: Of the total 197 children, 174 had reached puberty. There were no significant differences between the groups in respect of testicular sizes and the prevalence of pubertal status among the groups (84.3% of NAFLD vs. 70.6% of non-NAFLD vs. 98.7% of control subjects). No significant differences were found in respect of gonadotropins and AMH levels. Total testosterone levels in the NAFLD group were significantly lower than those of the non-NAFLD obese group (P < 0.001) and the control group (P < 0.001). Inhibin B levels were also significantly lower in all (NAFLD and non-NAFLD) obese groups compared to the control group (P = 0.008). Conclusions: The results of the study demonstrated that diminished testosterone and inhibin B levels occur in pubertal obese boys with NAFLD. No significant differences were detected according to pubertal status, AMH levels, and testicular volumes in the age-matched groups.