Blossom-end rot (BER) in tomato has been generally reported as a calcium (Ca)-related physiological disorder influenced by cultivar and environmental factors. In our previous works, we found that different fruit-sized cultivars could share a similar threshold value of water-soluble Ca. In addition, seasonal susceptibility to BER was closely related to fruit growth rate. This study aimed to clarify the effect of fruit growth rate as a dominant factor determining the susceptibility in different fruit-sized tomato cultivars. A large-sized cultivar, ‘Momotaro Fight’, and medium-sized ‘Cindy Sweet’, with different susceptibility to BER disorder, were hydroponically grown with modified Hoagland nutrient solutions consisting of a range of Ca:K (potassium) ratios in four cropping seasons. In spring and summer, BER incidence was more than 60 and 10% in ‘Momotaro Fight’ and ‘Cindy Sweet’, respectively, when plants were fed with low Ca. BER was rarely observed when water-soluble Ca exceeded 0.30 μmol·g−1 FW, and the rate of BER incidence increased with a decrease in water-soluble Ca concentration in both cultivars. Fruit growth rate was much more vigorous in ‘Momotaro Fight’ than ‘Cindy Sweet’, especially in summer. It was significantly favored by the increased temperature and solar radiation in both cultivars. The multiple regression analyses detected a significant effect of fruit growth rate on BER incidence, exclusively in ‘Momotaro Fight’. Together with water-soluble Ca, fruit growth rate explained over 50% of the variation of BER incidence. A vigorous rate of fruit growth can play a more important role in decreasing water-soluble Ca in ‘Momotaro Fight’, and result in severe and frequent BER incidence, compared to ‘Cindy Sweet’. Thus the cultivar difference in the susceptibility to BER is likely explained by the difference in the growth rate of young fruit affecting water-soluble Ca in the distal part of tomato fruit.