Coffee consumption is increasing globally. We aimed to assess the effect of coffee consumption on the risk of all-cause and cause-specific mortality in a pooled analysis of eight population-based cohort studies in Japan (Japan Cohort Consortium). Data came from eight Japanese cohort studies (144,750 men and 168,631 women). During a mean follow-up time of 17 years, 52,943 deaths occurred. More specifically, 19,495 cancer deaths, 7321 deaths due to heart disease, 6387 cerebrovascular, 3490 respiratory disease and 3382 injuries and accidents. A random effects model was applied to obtain pooled hazard ratios (HRs) and 95% confidence intervals (95%CIs). In both sexes, coffee consumption up to 5 cups/day was overall protective in relation to all-cause mortality, with the association attenuating in the highest category of coffee consumption (≥5 cups/day). In men, a similar inverse association was observed for major causes of mortality except cancer. In women, coffee consumption decreased the risk for mortality due to heart disease in the 1-2 cups/day category, but increased the risk in the ≥5 cups/day category. Coffee consumption was not associated with cancer in both sexes. Results were similar among male current smokers and female never-smokers. Based on available data, this pooled analysis suggests that coffee consumption under five cups per day may be beneficial for reducing the risk of mortality due to major causes.