Myiasis is considered a serious medical condition in animals and humans that occurs predominantly in tropical countries. Cochliomyia hominivorax is one of the main fly species that causes myiasis and the actual geographic distribution includes the Caribbean and all of South America, except Chile. The use of synthetic insecticides and endectocides in livestock for the myiasis treatment has resulted in insect resistance, while also causing residuals in the environment and contamination of animal food products. Biologically active compounds are considered an alternative for the sustainable management of insects, as they are biodegradable and less damaging to the environment. This study developed a nanoemulsion containing the essential oil of Baccharis dracunculifolia and evaluated its in vitro effects on C. hominivorax larvae. High pressure homogenization was used to develop the nanoemulsion. Larvicidal tests were carried out with the tested products using 15 larvae/repetition, for a total of 150 larvae per treatment. Five different concentrations of the nanoemulsion were tested shortly after preparation and after 120 days of storage. For the fresh formulation, at concentrations of 5, 7.5, 10, 13.5, and 15% (w/v) we found mortality of 28, 48, 70, 84, and 97%, respectively, while for the stored formulation, we found mortality of 17, 36, 51, 81, and 92%. The larvicidal effect was similar, except for the concentrations of 5 and 10% (w/v) (p < 0.05). Our results show that the natural based B. dracunculifolia nanoemulsion can be considered a promising alternative for the treatment and control of myiasis caused by C. hominivorax.