Prevalent irregular rainfall, flooding for weed control, and unleveled fields in the middle and lower reaches of the Yangtze River all contribute to flooding stress on germination and growth of direct-seeded rice (Oryza sativa L.). Herein, some experiments were conducted so as to assess the effects of seed priming with selenium (Se) on the germination and growth of rice under hypoxia. The experiment was arranged in a completely randomized factorial design with two factors and five replicates. Factors included Se concentration (0, 30, and 60 μmol/L) and duration of flooding stress (0, 2, 4, and 8 days). The experimental results showed that Se accelerated seed germination and increased emergence index and final emergence percentage. Additionally, Se increased shoot and root lengths and dry weights, but high Se concentration (60 μmol/L) reduced 18-day-old seedling dry weight under long-term flooding (8 days). Furthermore, Se reduced malondialdehyde content and increased starch hydrolysis efficiency in seeds, superoxide dismutase, peroxidase, catalase, and glutathione peroxidase activities and seedling soluble protein and total chlorophyll contents. Se improved seedling total Se and organic Se contents while increasing total dry weight and yield. Notably, the highest yield was obtained after a 4-day flooding period. Although Se priming favored rice seedling emergence and growth under flooding conditions, Se concentrations equal or above 60 μmol/L increased the risk of seedling death during long-term flooding (≥8 days).