BACKGROUND: Night shift work has well-known adverse effects on health. However, few studies have investigated the relationship between thyroid diseases and night shift work. This study aimed to examine night shift workers and their changes in thyroid stimulating hormones (TSH) levels over time. METHODS: Medical check-up data (2011–2015) were obtained from 967 female workers at a university hospital in Incheon, Korea. Data regarding TSH levels were extracted from the records, and 2015 was used as a reference point to determine night shift work status. The relationships between TSH levels and night shift work in each year were analyzed using the general linear model (GLM). The generalized estimating equation (GEE) was used to evaluate the repeated measurements over the 5-year period. RESULTS: The GEE analysis revealed that from 2011 to 2015, night shift workers had TSH levels that were 0.303 mIU/L higher than the levels of non-night shift workers (95 % CI: 0.087–0.519 mIU/L, p = 0.006) after adjusting for age and department. When we used TSH levels of 4.5 ≥ mIU/L to identify subclinical hypothyroidism, night shift workers exhibited a 1.399 fold higher risk of subclinical hypothyroidism (95 % CI: 1.050–1.863, p = 0.022), compared to their non-night shift counterparts. CONCLUSIONS: This result of this study suggests that night shift workers may have an increased risk of thyroid diseases, compared to non-night shift workers.