Background: There is evidence supporting electroacupuncture (EA) for the treatment of major depressive disorder (MDD), but its characteristics have not been well investigated. Objective: To investigate the effectiveness and characteristics of EA in MDD. Methods: 60 subjects were enrolled-35 in the EA group and 25 in the selective serotonin reuptake inhibitor (SSRI) group based on their preferences-in an 8-week non-randomised controlled clinical trial. The 24-item Hamilton depression rating scale (HAMD-24) and clinical global impression (CGI) were adopted for clinical assessment. The Columbia suicide severity rating scale and adverse event form were used to measure safety and tolerability. The characteristics of EA and SSRIs were compared by analysing seven factors of the HAMD-24. Results: There was no significant difference between the two groups in terms of HAMD-24 response rate after intervention (P>0.05). Patients treated with EA demonstrated a significant reduction in CGI scores (P<0.05) with fewer adverse events compared with SSRIs (P<0.01). Although HAMD-24 factor analysis showed both EA and SSRIs could improve factor scores in cognitive impairment, diurnal variation, retardation, sleep disturbance, anxiety/somatisation and feelings of despair, EA showed greater improvement in anxiety/somatisation and feelings of despair than SSRIs (P<0.05). Conclusions: There was no significant difference between EA and SSRIs in the treatment of MDD with respect to our primary outcome. However, as a potential therapy for MDD, EA appeared to result in greater symptom improvement than SSRI treatment with respect to anxiety/somatisation and feelings of despair. The results of this secondary analysis should be interpreted cautiously given the inherent issues of multiple testing.