We examined the association of dietary non-enzymatic antioxidant capacity (NEAC) in overall diet, and separately from foods and beverages, with serum liver enzymes in a Japanese working population. This cross-sectional study was conducted among 1791 employees aged 18–69 years, who underwent a comprehensive health checkup in 2012–2013. A brief validated self-administered diet-history questionnaire was used for dietary assessment, and dietary NEAC intake was determined from databases of NEAC values, obtained using ferric reducing-antioxidant power (FRAP) and oxygen radical absorbance capacity (ORAC) assays. The dietary NEAC intake was calculated by multiplying the estimated NEAC values by the amounts consumed and summing the resulting values. A multiple-regression analysis was performed to explore the association between dietary NEAC intake and the serum levels of liver enzymes (aspartate aminotransferase (AST), alanine aminotransferase (ALT), and gamma-glutamyltransferase (GGT)), after adjustment for confounding factors. No significant associations were found between overall dietary NEAC intake and AST (FRAP, p for trend = 0.97; ORAC, p = 0.72), ALT (FRAP, p = 0.73; ORAC, p = 0.92), and GGT (FRAP, p = 0.96; ORAC, p = 0.19) levels. Food-derived, but not beverage-derived, NEAC intake was inversely associated with serum GGT levels (FRAP, p for trend = 0.001; ORAC, p = 0.02), particularly among older participants and those with high serum ferritin concentrations. The results imply that overall dietary NEAC intake is not associated with liver dysfunction, and that the NEAC values from foods may be inversely associated with serum GGT levels.