Perinatal depression affects one-third of pregnant women living with HIV (WLH). We examined patterns of treatment response to a novel stepped model of depression care among WLH with perinatal depression in Uganda. As part of the Maternal Depression Treatment in HIV (M-DEPTH) cluster randomised controlled trial, 191 women were enrolled across four antenatal care clinics assigned to provide stepped care including behavioural and antidepressant therapy (ADT), and another 200 across four clinics assigned to provide usual care. They were assessed for depression severity using the Patient Health Questionnaire (PHQ-9) at enrolment and multiple times over 12 months of follow-up. We used repeated measures latent class analysis (LCA) to identify discrete trajectories of depression symptoms, while multinomial regression analyses measured correlates of class membership. The LCA identified three trajectories among those in the treatment group: mildly depressed individuals who improved (MiD-I) (n = 143, 75%), moderately depressed individuals who improved (MoD-I) (n = 33, 17%), and moderately depressed individuals who remained depressed (MoD-R) (n = 15, 8%). Membership in MiD-I was associated with lower levels of intimate partner violence at baseline (P = 0.04) and month 6 (P < 0.001), and less recent trauma exposure (P = 0.03) at baseline. At month 6, social support was lowest in MoD-R, while the degree of negative problem-solving orientation was highest (both P < 0.001) in this class. The LCA also identified three trajectories among those in the usual care comparison group: mildly depressed (MiD) (n = 62, 31%), moderately depressed (MoD) (n = 71, 35%), and seriously depressed (SiD) (n = 67, 34%), with each experiencing slight improvement. Recent traumas at baseline were highest in SiD (P < 0.001); this group also reported the lowest positive problem-solving orientation and highest negative problem-solving orientation (P < 0.001) at baseline. Depression symptom trajectories among women with perinatal depression are related to modifiable factors such as problem-solving orientation and interpersonal dynamics, with the latter including intimate partner violence and social support. Most treatment recipients were characterised by trajectories indicating recovery from depression. ClinicalTrials.Gov (NCT03892915).