The prevalence of allergic diseases has been increasing globally prior to COVID-19. The pandemic resulted in changes in lifestyle and personal habits such as universal mask-wearing and social distancing. However, there is insufficient information on the impact of the COVID-19 pandemic on the prevalence of allergic conditions such as asthma, atopic dermatitis, and allergic rhinitis. We analyzed the incidence rate for self-reported and doctor-diagnosed cases of allergic diseases of asthma, atopic dermatitis, and allergic rhinitis. A total of 15,469 subjects were registered from a national cohort dataset of the National Health and Nutrition Examination Survey. Using multiple logistic regression analysis, we calculated the adjusted odds ratio (OR) for each disease in 2020 compared to 2019. Subgroup analyses were performed according to age and sex. There were no statistically significant differences between the incidence of doctor-diagnosed and current allergic diseases in 2019 and 2020 (asthma, p = 0.667 and p = 0.268; atopic dermatitis, p = 0.268 and p = 0.973; allergic rhinitis, p = 0.691 and p = 0.942, respectively), and subgroup analysis showed consistent results. Among the Korean population from 2019 to 2020, the incidence of the allergic diseases asthma, atopic dermatitis, and allergic rhinitis did not decrease as expected.