Background: Hypothyroidism has several symptoms (weight gain, arrhythmias, mood changes, etc.). The aims of this study were (1) to assess the prevalence of anxiety and depression in levothyroxine-treated hypothyroid women and in women without hypothyroidism; (2) to identify variables associated with anxiety and depression. Methods: A case-control study was performed with 393 women. Case-group: 153 levothyroxine-treated hypothyroid women. Control-group: 240 women without hypothyroidism. Convenience sampling. Instrument: The Hamilton Hospital Anxiety and Depression Scale (HADS), and a sociodemographic questionnaire. Results: The prevalence of anxiety in levothyroxine-treated hypothyroid women was higher than in women without hypothyroidism (29.4% vs. 16.7%, χ2p < 0.001). The prevalence of depression in the case group was higher than in the control group (13.1% vs. 4.6%, χ2p < 0.001). Levothyroxine-treated hypothyroid women were more likely to have anxiety (OR = 2.08, CI: 1.28-3.38) and depression (OR = 3.13, IC = 1.45-6.45). Conclusion: In spite of receiving treatment with levothyroxine, women with hypothyroidism are more likely to have depression and anxiety. Health professionals need to assess the mood of women with hypothyroidism. Although levothyroxine is a good treatment for the symptoms of hypothyroidism, it may not be enough to prevent development or persistence of depression and anxiety by itself.