In worldwide production, rice is the second-most-grown crop. It is considered a staple food for many populations and, if naturally enriched in Se, has a huge potential to reduce nutrient deficiencies in foodstuff for human consumption. This study aimed to develop an agronomic itinerary for Se biofortification of Oryza sativa L. (Poaceae) and assess potential physicochemical deviations. Trials were implemented in rice paddy field with known soil and water characteristics and two genotypes resulting from genetic breeding (OP1505 and OP1509) were selected for evaluation. Plants were sprayed at booting, anthesis and milky grain phases with two different foliar fertilizers (sodium selenate and sodium selenite) at different concentrations (25, 50, 75 and 100 g Se·ha−1). After grain harvesting, the application of selenate showed 4.9–7.1 fold increases, whereas selenite increased 5.9–8.4-fold in OP1509 and OP1505, respectively. In brown grain, it was found that in the highest treatment selenate or selenite triggered much higher Se accumulation in OP1505 relatively to OP1509, and that no relevant variation was found with selenate or selenite spraying in each genotype. Total protein increased exponentially in OP1505 genotype when selenite was applied, and higher dosage of Se also increased grain weight and total protein content. It was concluded that, through agronomic biofortification, rice grain can be enriched with Se without impairing its quality, thus highlighting its value in general for the industry and consumers with special needs.