Individuals with atrial fibrillation (AF), especially women, have an increased risk of stroke and death. Although hormone replacement therapy (HRT) is widely used in postmenopausal women, the association between HRT use and AF risk is unclear. We aimed to investigate the association between various types of HRT and AF. This was a population-based retrospective cohort study from The Korean National Health Insurance Service-National Sample Cohort (2004–2015). Participants were aged 45–60 years and were free from cardiovascular disease and AF at baseline. Overall, 13,452 (64.03%) women had never received HRT, 5671 (26.99%) had received HRT, and 1885 (8.98%) were currently receiving HRT. In multivariable analysis, the relative hazards for AF were significantly higher among current users (p < 0.001) and lower among past users (p = 0.069). Current users—except those using estradiol-only HRT—had significantly elevated AF risk. Among past users, only estradiol plus progestin HRT users had a reduced AF risk after adjusting for covariates (p = 0.027). Ongoing HRT posed an increased risk of AF. The degree of risk varied based on the specific type of estrogen and progestins co-administration. These findings indicate that, with respect to AF risk, oral estradiol-containing HRT is superior to HRT containing oral conjugated equine estrogen or tibolone.