Hypertension has become a major public health issue worldwide. Whole grains contain higher levels and a broader range of nutrients with potential health benefits and may decrease the risk of hypertension. However, no prospective studies have investigated this association in the high-income Asia Pacific region, which has the lowest whole grain intake worldwide. Thus, we examined the prospective association between whole grain consumption and the development of hypertension in Japan. Participants included 944 working Japanese adults aged 19–68 years who had no hypertension at baseline and completed a 3-year follow-up survey. Whole grain consumption was assessed via a self-administered dietary questionnaire. Multivariate logistic regression analysis was carried out to examine the association between whole grain consumption and hypertension, adjusting for potential confounding factors, such as sociodemographic, lifestyle, dietary, and occupational characteristics. After 3 years, 9.4% (86 cases) of the study participants had developed hypertension. More frequent whole grain consumption, classified as an intake frequency of “sometimes or always”, was associated with lower odds of hypertension (multivariate-adjusted odds ratio: 0.36; 95% confidence interval: 0.16–0.83; p for trend = 0.04) compared with no consumption. Consuming more whole grains may decrease the risk of developing hypertension.