Selenium is a trace nutrient that has both nutritional and nutraceutical functions, whereas narrow nutritional range of selenium intake limits its use. Selenium nanoparticles (SeNPs) are less toxic and more bioavailable than traditional forms of selenium, suggesting that SeNPs have the potential to replace traditional selenium in food industries and/or biomedical fields. From the perspective of how SeNPs can be applied in health area, this review comprehensively discusses SeNPs in terms of its preparation, nutritional aspect, detoxification effect of heavy metals, nutraceutical functions and anti-pathogenic microorganism effects. By physical, chemical, or biological methods, inorganic selenium can be transformed into SeNPs which have increased stability and bioavailability as well as low toxicity. SeNPs are more effective than traditional selenium form in synthesizing selenoproteins like glutathione peroxidases. SeNPs can reshape the digestive system to facilitate digestion and absorption of nutrients. SeNPs have shown excellent potential to adjunctively treat cancer patients, enhance immune system, control diabetes, and prevent rheumatoid arthritis. Additionally, SeNPs have good microbial anti-pathogenic effects and can be used with other antimicrobial agents to fight against pathogenic bacteria, fungi, or viruses. Development of novel SeNPs with enhanced functions can greatly benefit the food-, nutraceutical-, and biomedical industries.