Heat stress during ripening increases the formation of chalky or cracked rice grains, and its occurrence is increasing, possibly owing to climate change. Silicon is known to improve water use efficiency, photosynthetic ability, and root vitality of rice plants, resulting in increased yields and grain quality. However, its effect on the formation of chalky or cracked rice grains remains unclear. We aimed to clarify the effect of silicate fertilizer on grain quality of brewers’ rice cultivar ‘Toyonishiki,’ which exhibits a low tolerance to high temperature. High air temperatures during ripening in 2015 and 2016 reduced grain quality of ‘Toyonishiki.’ The application of silicate fertilizer significantly increased silicon concentration in hulls and leaves and increased the number of panicles relative to the control (no silicate fertilizer). Silicate fertilizer significantly reduced the occurrence of chalky and cracked grains, which were significantly negatively correlated with the silicate content of plants. In addition, the water uptake ability of roots and the stomatal conductance of leaves during ripening tended to increase with the application of silicate fertilizer. We consider that silicate fertilizer improved water use efficiency and photosynthetic activity of rice plants, even under high temperatures during ripening. In addition, we conclude that the application of silicate fertilizer mitigated the production of chalky and cracked grains of brewers’ rice cultivar ‘Toyonishiki.’