The amount of specific trace elements like selenium (Se) may be of health concern for humans if contained in too high (or low) quantities in staple foods like rice. Among the attempts aimed to optimize the Se concentration in rice, only few studies have been focused on the use of irrigation methods other than continuous flooding. Since intermittent irriguous methods, like sprinkler and saturation, have found to be effective in modifying the bioaccumulation of arsenic and cadmium in rice kernels, the main goal of this study is to measure the amount of the total Se contained in grains of 26 rice genotypes cultivated for two consecutive agrarian vintages in the same open field and with the same water, but differently irrigated with continuous flooding, sprinkler or saturation. To do this, an original and validated ICP-MS method has been developed. The validation parameters accounted for a high sensitivity and accuracy. Sprinkler irrigation is able to reduce in the average of 90% the amount of total Se in kernels in comparison to values measured in rice irrigated with continuous flooding. In conclusion, different irrigation techniques and rice genotypes seem to be valuable tools in order to allow in the future the customized modulation of the Se concentration in rice grain according to the needs of the various populations.