Few studies have reported the association between the Japanese diet as food score and mortality. This study aimed to investigate adherence to the Japanese food score associated with all-cause, CVD and cancer mortality. A total of 58 767 (23 162 men and 34 232 women) Japanese participants aged 40–79 years, who enrolled in the Japan Collaborative Cohort Study between 1988 and 1990, were included. The Japanese food score was derived from the components of seven food groups (beans and bean products, fresh fishes, vegetables, Japanese pickles, fungi, seaweeds and fruits) based on the FFQ. The total score ranged from 0 to 7, and participants were divided into five categories based on scores (0–2, 3, 4, 5 and 6–7). Hazard ratios (HR) and 95 % CI for all-cause, CVD and cancer mortality based on sex were estimated using Cox proportional models. During the follow-up period until 2009, 11 692 participants with all-cause, 3408 with CVD and 4247 with cancer died. The multivariable HR in the 6–7 and 0–2 Japanese food score groups were 0·93 (95 % CI 0·86, 1·01) in men and 0·82 (95 % CI 0·75, 0·90) in women for all-cause mortality and 0·89 (95 % CI 0·76, 1·04) in men and 0·66 (95 % CI 0·56, 0·77) in women for CVD mortality. Our findings suggest that adherence to the Japanese food score consisting of food combinations characterised by a Japanese diet may help in preventing all-cause and CVD mortality, especially in women.