Nonalcoholic fatty liver disease (NAFLD) is associated with low testosterone levels in serum. The aim of this study was to evaluate the effect of apple vinegar on fertility indices in a rat model of NAFLD. To study this effect, 32 adult male rats were divided into four groups: A-normal diet, B-high-fat diet (HFD), C-apple vinegar and D-HFD plus apple vinegar. At the end of the week 22, the Lee index, serum lipid profiles, liver enzymes, glucose and total antioxidant levels (TAC) in serum were determined. In addition, liver and testis tissue homogenate, histopathology, serum testosterone and sperm parameters were measured and HOMA-IR calculated. Significant reduction in Lee index, serum triglyceride, cholesterol, liver enzymes and glucose levels was observed in vinegar treated group compared with HFD group. Vinegar lowered insulin resistance compared with HFD (p < 0.01). Steatosis in hepatocytes reduced from 56% in HFD group to 20% in group D (p < 0.05). Vinegar caused a significant increase in serum testosterone, improvement in sperm parameters and a reduced germ cell apoptosis (p < 0.05). There was an insignificant increase in TAC levels in the serum and homogenate tissue of liver and testis compared with HFD. This study reports apple vinegar has beneficial effects on male rat fertility indices in an in vivo model of NAFLD.