Youth is defined as a period of transition from childhood to adulthood that ranges between the ages of 15 and 24, and it is the most mobile social group in the world. Youth migration in El Salvador and Honduras is a well-known problem; however, limited research has studied the causes of migration and the impact of agricultural education programs on the decision to migrate. This study aims to identify and compare the migration intentions of students in agricultural and non-agricultural programs of two rural communities of El Salvador and Honduras. For this quantitative study, a two-group model was used, the target population (N = 209) was composed of high school students with similar socioeconomic characteristics. Overall, the comparison between El Salvador and Honduras showed a significant difference between countries regarding their migration intentions (p < 0.05). Salvadorian students presented a stronger willingness to migrate. Moreover, students’ intention of migration was evaluated based on their educational background. Youth who were not part of a formal agricultural program have a higher intention of migrating (p < 0.05). Finally, the main and interaction effects of intention to migrate, country of origin, and academic program based on the different migration drivers were analyzed.