Nanotechnology has been increasingly used in plant sciences, with engineered nanoparticles showing promising results as fertilizers or pesticides. The present study compared the effects in the foliar application of Se nanoparticles (SeNPs) or sodium selenite-Se(IV) on rice seedlings. The degree of plant growth, photosynthetic pigment content, and concentrations of Se, Na, Mg, K, Ca, Mn, Co, Cu, Zn, As, Cd, and Pb were evaluated. The results showed that the application of SeNPs at high concentrations (5 mg L-1), as well as the application of Se(IV), inhibited plant growth and increased the root concentrations of As and Pb. The application of SeNPs at 0.5 mg L-1 significantly increased Se accumulation in the aerial part from 0.161 ± 0.028 mg kg-1 to 0.836 ± 0.097 mg kg-1 without influencing physiological, chemical, or biochemical parameters. When applied to leaves, SeNPs tended to remain in the aerial part, while the application of Se(IV) caused a higher Se translocation from the shoots to the roots. This study provides useful information concerning the uptake, accumulation, and translocation of different Se formulations in rice seedlings and their effect on plant ionomic profiles, thus showing that the foliar application of SeNPs at low concentrations can be an effective and safe alternative for rice biofortification.