Pest fly species and abundance, fly avoidance behaviours, grazing behaviour, milk cortisol, and milk production were studied to understand the impact of pest flies on dairy cows at pasture. Treatment of cows with a natural fly repellent based on sunflower oil and essential oils, lemongrass and geranium, was used to compare cows with reduced fly attack intensity to untreated cows. Treatment of cows with the fly repellent resulted in a 69.5 % reduction in pest fly attack intensity. Treated cows also had reduced rates of tail flicks, skin twitches, head throws, and leg stamps by 44.8 %, 54.0 %, 78.9 %, and 45.1 % respectively. The reduction of flies on treated cows had no effect on milk cortisol and milk production. Treatment of cows with an effective, natural fly repellent may improve cow comfort with reduced levels of painful biting flies and fly avoidance behaviours.