Background: Sleep duration is an identified risk factor for adverse health outcomes. As the endocrine system is closely intertwined with sleep duration and quality, the association between endocrine dysfunction and sleep has been evaluated. Thyroid function, particularly that related to thyrotropin (TSH), is also known to be influenced by the sleep/awake status and circadian rhythm. Additionally, a link between sleep duration and autoimmunity, which is a common cause of thyroid dysfunction, has been suggested; however, depending on the sleep deprivation method used in studies, the effects of sleep on thyroid function vary. The relationship between subclinical thyroid dysfunction and sleep duration is poorly documented. Thus, to elucidate the impact of sleep on thyroid function, we investigated the association of subclinical thyroid dysfunction with sleep duration using representative data from the sixth Korea National Health and Nutrition Examination Survey, conducted from 2013 to 2015. Methods: In all, 4945 participants (2543 male and 2402 female) were included after excluding subjects using the following criteria: <19 years of age, free T4 level outside the normal range, history of thyroid disease, or incomplete data. The population was classified into three groups: short sleeper (<7 h/day), normal sleeper (7–8 h/day), and long sleeper (>8 h/day). The odds ratio (OR) for subclinical hypothyroidism or hyperthyroidism according to sleep duration was evaluated. Results: The short, normal, and long sleeper groups consisted of 2097, 2514, and 334 subjects, respectively. On multiple logistic regression analysis, compared to normal sleepers, short sleepers showed a significantly increased risk of subclinical hyperthyroidism (OR 1.37, 95% confidential interval (CI) 1.02–1.84, p = 0.036), while the risk of subclinical hypothyroidism in short sleepers was not elevated. Comparing long sleepers to normal sleepers, the OR for subclinical hyperthyroidism and hypothyroidism was 1.79 (95% CI 1.12–2.86, p = 0.015) and 1.91 (95% CI 1.03–3.53, p = 0.039), respectively. Conclusions: Both shorter and longer sleep durations were associated with an increase in the risk of subclinical thyroid dysfunction compared to the optimal sleep duration. This analysis of representative population data shows that sleep duration could intertwine with thyroid function resulting in increased risk of subclinical thyroid dysfunction.