Background Hypothyroxinemia, i.e. Low free T4 with normal TSH level, which overlaps, to a great extent, with the laboratory criteria of central hypothyroidism, could be easily neglected, if attention is paid only to patients with elevated TSH. We aimed to assess the association between mirtazapine use and hypothyroxinemia in patients affected by major depressive disorder. Methods We conducted a retrospective cohort study in the Second Affiliated Hospital of Xinxiang Medical University between January 2016 and December 2018. Patients affected by major depression disorder and admitted to the hospital for treatment during the study period and had thyroid tests at admission and after treatment were included. Patients with abnormal thyroid function at baseline or received mood stabilizers or quetiapine during hospitalization were excluded. Mirtazapine use was the exposure measure, and hypothyroxinemia was as the primary outcome of this study. Log-binomial model was used to estimate the association between mirtazapine use and hypothyroxinemia, after adjusting for potential confounding factors. Results A total of 220 eligible patients were included in the final analysis. Of them, 88 used mirtazapine. The incidence of hypothyroxinemia in patients who used mirtazapine was higher (37.5%) than those patients who did not use (19.7%). The relative risk of developing hypothyroxinemia was 1.64 (95% confidence interval: 1.31-1.78) for mirtazapine use, after adjusting for confounding factors. Conclusion Mirtazapine use was associated with the risk of developing hypothyroxinemia. Clinicians should be aware that hypothyroxinemia may be neglected in patients treated by mirtazapine due to attention paid only to those with elevated TSH.