Despite the high correlation between anxiety and depression, little remains known about the course of each condition when presenting concurrently. This study aimed to identify longitudinal patterns during antidepressant treatment in patients with depression and anxiety, and evaluate related factors associated with these patterns. By analyzing longitudinal self-report Patient Health Questionnaire-9 (PHQ-9) and General Anxiety Disorder-7 (GAD-7) scores that tracked courses of depression and anxiety over a three-month window among the 577 adult participants, six depression and six anxiety trajectory subgroups were computationally derived using group-based trajectory modeling. Three depression subgroups showed symptom improvement, while three showed nonresponses. Similar patterns were observed in the six anxiety subgroups. Multinomial regression was used to associate patient characteristics with trajectory subgroup membership. Compared to patients in the remission group, factors associated with depressive symptom nonresponse included older age and lower depression severity.