This systematic review and meta-analysis elucidate the effects of the Japanese-style diet and characteristic Japanese foods on the mortality risk of cardiovascular disease (CVD), cerebrovascular disease (stroke), and heart disease (HD). This review article followed the PRISMA guidelines. A systematic search in PubMed, The Cochrane Library, JDreamIII, and ICHUSHI Web identified prospective cohort studies on Japanese people published till July 2020. The meta-analysis used a random-effects model, and heterogeneity and publication bias were evaluated with I2 statistic and Egger’s test, respectively. Based on inclusion criteria, we extracted 58 articles, including 9 on the Japanese-style diet (n = 469,190) and 49 (n = 2,668,238) on characteristic Japanese foods. With higher adherence to the Japanese-style diet, the pooled risk ratios (RRs) for CVD, stroke, heart disease/ischemic heart disease combined (HD/IHD) mortality were 0.83 (95% CI, 0.77–0.89, I2 = 58%, Egger’s test: p = 0.625, n = 9 studies), 0.80 (95% CI, 0.69–0.93, I2 = 66%, Egger’s test: p = 0.602, n = 6 studies), and 0.81 (95% CI, 0.75–0.88, I2 = 0%, Egger’s test: p = 0.544, n = 6 studies), respectively. Increased consumption of vegetables, fruits, fish, green tea, and milk and dairy products decreased the RR for CVD, stroke, or HD mortality. Increased salt consumption elevated the RR for CVD and stroke mortality. Increased consumption of dietary fiber and plant-derived protein decreased the RR for CVD, stroke, and HD/IHD mortality. The Japanese-style diet and characteristic Japanese foods may reduce CVD mortality. Most studies conducted diet surveys between 1980 and the 1990s. This meta-analysis used articles that evaluated the same cohort study by a different method. A new large-scale cohort study matching the current Japanese dietary habits is needed to confirm these findings.