Several studies have reported that short sleep duration is a risk factor for obesity and metabolic disease. Moreover, both sleep duration and sleep timing might independently be associated with dietary nutrient intake. In this study, we investigated the associations between self-reported sleep duration and dietary nutrient intake, with and without adjustments for variations in sleep timing (i. e., the midpoint of sleep). We conducted a questionnaire survey, comprising a validated brief self-administered diet history questionnaire (BDHQ) and the Japanese version of the Pittsburgh Sleep Quality Index (PSQI) among 1902 healthy Japanese adults and found that the dietary intakes of several nutrients correlated with sleep duration among men regardless of adjustment for the midpoint of sleep. Particularly, (1) small but significant correlations were observed between sleep duration and the percentage of energy from protein, regardless of adjustment for the midpoint of sleep; (2) energy-adjusted intakes of sodium, vitamin D, and vitamin B12 also significantly correlated with sleep duration; and (3) intakes of bread, pulses, and fish and shellfish correlated with sleep duration. In contrast, no significant correlations were observed between sleep duration and dietary intakes among women. This study revealed that after controlling for the midpoint of sleep, sleep duration correlated significantly with the dietary intake of specific nutrients and foods in a population of Japanese men.