The aim of this study was twofold: to identify different emotional intelligence (EI) profiles and to verify possible statistically significant differences in school refusal factors that result in a demotivation to attend school. Participants were 2362 Chilean adolescents aged from 13 to 17 (M = 15.25; SD = 1.33), who completed the Trait Meta-Mood Scale-24 (TMMS-24) and the School Refusal Assessment Scale-Revised (SRAS-R). Cluster analysis identified four EI profiles: high scores in repair and low in attention, high scores in attention and low in clarity and repair, low EI and high EI. Students with high scores in attention and low in repair scored higher in the first three factors of the SRAS-R, whereas in the fourth factor of the SRAS-R, students with high EI had significantly higher scores. Emotional regulation seems to be one of the determinant factors to prevent the appearance of school refusal. Based on these findings, we recommend that EI training be a part of future programs to overcome school attendance demotivation issues.