The food and beverage industry often need to encapsulate hydrophobic functional ingredients in their products, including colors, flavors, lipids, nutraceuticals preservatives, and vitamins. Encapsulation can improve the handling, water-dispersibility, chemically stability, and efficacy of these functional ingredients. In this review article, we focus on the design of nanoemulsion-based delivery systems to encapsulate, protect, and deliver nonpolar bioactive agents, such as vitamin A, D and E, bcarotene, lycopene, lutein, curcumin, resveratrol, and coenzyme Q10. Initially, the challenges associated with incorporating these different bioactives into foods are highlighted. The relative merits and drawbacks of different nanoemulsion fabrication methods are then discussed. Finally, examples of the application of nanoemulsions for improving the stability and bioavailability of various kinds of hydrophobic vitamins and nutraceuticals are provided.