Background: There are some evidences on adverse effects of reducing thyroid hormones levels on appearing cognition. The present study aimed to assess cognitive function in patients with hypothyroidism under-treated with routine hormone replacement therapy compared to healthy euthyroid individuals. Methods: Thirty consecutive hypothyroid female patients aged 25 to 40 years who referred to endocrinology and metabolism clinic at Rasoul-e-Akram hospital in Tehran within a four-year period in 2015 were assessed. Also, thirty healthy euthyroid subjects matched for sex, age, and educational level were selected as the control. For assessment of cognitive function status, the Mini Mental Status Exam (MMSE) was used. Results: The study showed lower mean cognitive score in hypothyroid patients when compared to euthyroid ones (25.33 ± 3.90 versus 29.40 ± 1.80, p = 0.010). Regarding association between cognition deficit and patients’ baseline characteristics, except for educational level that was positively associated with cognition score (p < 0.001), no significant association was revealed between mean cognition score and other parameters including age (p = 0.569), occupation status (p = 0.631), and marital status (p = 0.859). According to the Bonferroni correction analysis, lower cognitive function was revealed in those with primary educational levels than those who with college degrees. Conclusion: Clinical hypothyroidism is potentially association with cognition deficit especially in those with lower educational level.