Flaxseed oil as a natural ingredient has many health benefits due to the rich contents of omega‐3 fatty acids. However, its use in food formulations is limited because of low aqueous solubility, easy oxidation owing to the unsaturated nature of the fatty acids such as omega‐3. The aim of this study was to prepare a stable nanoemulsion containing flaxseed oil and investigate the fortification of yogurt with this nanoemulsion compared with fortification with bulk flaxseed oil. The nanoemulsion of flaxseed oil‐in‐water was obtained by low‐energy emulsification method. Optimized nanoemulsion contains 3% (w/w) flaxseed vegetable oil, 36% (w/w) surfactant, 10% (w/w) co‐surfactant, and 51% (w/w) deionized water as a continuous phase. The result of transmission electron microscopy (TEM) showed that the optimal size was about 60 nm, which was stayed stable for 11 months. The results of gas chromatography (GC) indicated that the amount of omega‐3 in nanoemulsion containing flaxseed oil was 27.3% and 19.8% after 7 days and 11 months, respectively. The turbidity results indicated the transparency of nanoemulsion after 11 months as well. The results of centrifuge experiments and thermal stress cycles exhibited that the optimized nanoemulsion was physically stable without any sign of creaming, phase separation, and cracking. In addition, pH and acidity of the yogurt fortified with nanoemulsion containing flaxseed oil were 4.22 and 1.41 wt%, respectively. In conclusion, fortifying yogurt with the nanoemulsion containing flaxseed oil can be considered as a solution to increase solubility, bioavailability, and protection of omega‐3.