Important factors in learning science include motivational variables (relevance of science learning for personal goals, self-efficacy for learning science, and interest in a scientific career), emotional variables (boredom and enjoyment in science classes), and engagement variables (vigor, dedication, and absorption towards science studies). Data from 3034 Chilean and Spanish compulsory secondary education students was used to study the relationships between these variables, by means of a self-report questionnaire analyzed using structural equation modeling (SEM). The model, tested for goodness of fit, showed that motivational variables predict emotions in science classes and explained 43% of boredom variance and 67% of enjoyment variance. Motivational and emotional variables explained the 73% variance in engagement toward science studies. Also seen is the essential role played by emotions that mediate between motivational variables in science learning and engagement towards science studies. When promoting engagement towards science studies, these results can be used to increase relevance of science learning to personal goals, self-efficacy for learning science, and interest in a scientific career, besides reducing boredom, increasing enjoyment in science classes, and enhancing engagement towards science studies.