Non-alcoholic fatty liver disease (NAFLD), often complicated by type 2 diabetes mellitus (T2DM), is reported to be associated with diet habits, including eating speed, in the general population. However, the association between eating speed and NAFLD in patients with T2DM, especially sex difference, has not been reported so far. This cross-sectional study included 149 men and 159 women with T2DM. Eating speed was evaluated by a self-reported questionnaire and divided into three groups: fast, moderate, and slow eating. Nutrition status was evaluated by a brief-type self-administered diet history questionnaire. NAFLD was defined as the hepatic steatosis index ≥36 points. Body mass index and carbohydrate/fiber intake in the fast-eating group were higher than those in the slow-eating group in men, whereas this difference was absent in women. In men, compared with eating slowly, eating fast had an elevated risk of the presence of NAFLD after adjusting for covariates (odds ratio (OR) 4.48, 95% confidence interval (CI) 1.09–18.5, p = 0.038). In women, this risk was not found, but fiber intake was found to be negatively associated with the presence of NAFLD (OR 0.85, 95% Cl 0.76–0.96, p = 0.010). This study indicates that eating speed is associated with the presence of NAFLD in men but not in women.