Long-term variations in annual lightning deaths in Japan were examined in relation to the number of thunder days, on the basis of death statistics for 1909 to 2014, and police data for 1968 to 2009. The number of lightning deaths was mostly 20 to 60 people without a remarkable trend before World War II, while it rose to over 100 just after the war, and then decreased during the latter half of the 20th century to less than 10 in recent decades. For the period before 1970, the number of annual lightning deaths was positively correlated with that of warm-season thunder days (averaged over 39 stations) with a correlation coefficient exceeding 0.5. The correlation became low and insignificant after the 1980s as lightning mortality decreased, although a high correlation of 0.6-0.8 was maintained between lightning damages and thunder days. There was also a positive correlation of 0.4-0.6 between lightning deaths and warm-season mean temperature until the 1980s, corresponding to a weak correlation between thunder days and temperature.