Non-alcoholic fatty liver disease (NAFLD) is a multifactorial disease that involves a complex interaction between genetics, diet, and lifestyle, all of which combine to form the NAFLD phenotype. In Japan, medical nutrition therapy for NAFLD has not yet been established, so NAFLD patients are instructed in the dietary modifications used for type 2 diabetes mellitus (T2DM). Because points of difference may exist in the effects of dietary choices on NAFLD and T2DM, the present study aimed to compare and assess the dietary intake of Japanese individuals with NAFLD and T2DM. This cross-sectional study involved 219 patients (77 NAFLD subjects; 33 males, 44 females; 142 T2DM subjects: 76 males, 66 females) aged 40–79 years. Dietary intake was assessed using a validated self-administered diet history questionnaire. Among the results, the most notable in NAFLD patients relative to T2DM patients were: 1) the low intake of vegetables that can reduce the overall energy density; 2) the high consumption of fruits and confectionery containing simple carbohydrates such as fructose; and 3) BMI may be higher. We demonstrated differences in dietary selection between the two groups. NAFLD patients were more likely to have dietary habits that promote fat accumulation in the body.