Background: Social anxiety disorder, lack of emotional autonomy, and depression can all negatively affect the abilities and, ultimately, the fate of adolescents. Objectives: The present study aimed to investigate the effects of emotionally focused therapy (EFT) on the emotional autonomy and emotion regulation of students with depression symptoms. Methods: This quasi-experimental research adopted a pretest-posttest control group design with follow-up. The statistical population included all high school students with depression symptoms in Ahvaz, (Iran) in the academic year 2022–2023. The purposive sampling technique was employed to select 30 students with depression symptoms. They were then randomly assigned to an experimental group (n = 15) and a control group (n = 15). Participants in the experimental group attended ten 45-minute sessions of EFT once a week, whereas those in the control group were placed on a waiting list. The research instruments included the Emotional Autonomy Scale (EAS) and Emotion Regulation Questionnaire (ERQ). The obtained data were entered into the SPSS v23. The repeated measures analysis of variance (ANOVA) was then used to analyze the research data. A P-value of less than 0.05 was considered significant. Results: The mean ± SD of emotional autonomy, reappraisal, and suppression was 24.60 ± 3.96, 21.53 ± 2.99, and 18.93 ± 2.21 on the pretest, whereas it was 31.53 ± 4.30, 29.60 ± 2.47, and 12.00±2.00 on the posttest. According to the results, EFT enhanced emotional autonomy and improved emotion regulation strategies (i.e., reappraisal and suppression) in students with depression symptoms (P < 0.001). Conclusions: In conclusion, EFT managed to improve emotional autonomy and emotion regulation strategies in students with depression symptoms. EFT can be recommended as an effective intervention to improve emotion regulation in students with depression symptoms.