Abstract Background Sub-optimal patient medication knowledge, negative beliefs, and concerns about the potential of medications to cause harm are important contributory factors to non-adherence in patients with depression. Objectives To assess the effectiveness of a pharmacist intervention on antidepressant medication knowledge, necessity, and concerns beliefs in patients with depression. Methods A prospective interventional study (approval number: ABUCUHSR/2020/018) was carried out between April 2019 and March 2020 at the Federal Neuro-Psychiatric Hospital, Maiduguri, Nigeria. Patients were randomized into the usual care or intervention group. The intervention consisted of an educational programme, and data were collected at baseline, 3 months, and 6 months. Patient knowledge about medicines and beliefs about medicines questionnaires were used to assess patient knowledge and beliefs. Key findings A total of 49 (81.6%) and 52 (86.6%) participants completed the 6-month follow-up in the usual care and intervention groups, respectively. Significant improvements in mean medication knowledge scores of participants in the intervention group were observed at 3 months (P < .001) and 6 months (P < .001), respectively. Significant improvements in mean medication necessity and concerns belief scores of participants in the intervention group were also observed at 3 months (P < .001) and 6 months (P < .001), respectively. Medication knowledge (P < .001, partial η2 = 0.203), medication necessity (P < .001, partial η2 = 0.329), and medication concerns (P < .001, partial η2 = 0.163) positively changed with time. Conclusion Pharmacist intervention significantly improved antidepressant medication knowledge, necessity, and concerns beliefs in patients with major depressive disorder.