This narrative review presents examples of omega-3 fatty acids supplementation in horse nutrition. Fats are essential in equine nutrition, serving not only as an energy source but also as functional components influencing health. Among them, omega-3 polyunsaturated fatty acids (PUFAs), particularly EPA and DHA, play a key role in modulating inflammatory and metabolic processes. This review summarizes their effects on respiratory health, equine metabolic syndrome (EMS), musculoskeletal function, reproduction, and early development. Omega-3 supplementation has been shown to support airway inflammation in horses, especially when combined with low-dust management practices. In EMS, these fatty acids support insulin regulation and reduce systemic inflammation, although they are not curative. In the musculoskeletal system, omega-3s help limit inflammation and cartilage degradation. Their reproductive benefits include improved semen quality in stallions and enhanced fatty acid profiles in mare’s milk, supporting foal development. The proposed mechanisms of omega-3 fatty acids’ effect are also provided. Overall, omega-3 fatty acids are a valuable supplement in equine functional nutrition and disease management.