A great deal of attention has been focused on the various health benefits apparently associated with consumption of fish oil. The incorporation of fish oils in food products is becoming increasingly widespread and a large variety of products is being marketed. However, the use of fish oil as functional nutritional ingredients in foods has been limited by its oxidative susceptibility. In the present study, attempts were made to develop fish oil fortified cookies as healthy snack foods by incorporating fish oil microencapsulate. Microencapsulation of fish oil was done by spray drying. Commercially available milk was used to form micro sized complexes with fish oil. Fish gelatin/maltodextrin were used as a wall material for encapsulation. Fish oil was added in three forms (fish oil as such, fish oil-in-water emulsion and fish oil microencapsulate) for the preparation of cookies. Cookies prepared without incorporating fish oil was served as control. The physical, chemical and sensory attributes of cookies were evaluated. Encapsulation significantly (P < 0.05) decreased lipid oxidation in the cookies. The sensory evaluation of cookies showed significant (P < 0.05) difference in the overall acceptability. Results from this study, demonstrated the possibility of fish oil incorporation into cookies through emulsification and microencapsulation which may increase the intake of omega-3 fatty acids for nutritional benefits.