Summary Background Atopic dermatitis (AD) often manifests in early childhood and has variable disease course among individual patients. Previous studies regarding the natural course of AD have usually been of small sample size and were not based on nationwide populations. Objectives We aimed to find out the disease duration and remission rate of children with early‐onset AD (onset in the first 2 years of life) in Taiwan, and to determine whether the presence of allergic rhinitis (AR) or asthma affects the disease course. Methods The patients with early‐onset AD in a nationally representative cohort were selected using the National Health Insurance Research Database of Taiwan and were followed from birth to 10 years of age. Kaplan–Meier survival analysis was carried out to analyse the disease duration and remission of AD. Between‐group analysis using the log‐rank test was carried out to analyse the influence of risk factors on the disease course. Results Of the 1404 children with early‐onset AD, 19·4% had disease duration < 1 year and 48·7% had disease duration < 4 years. During the follow‐up, 69·8% of the patients went into remission. Sex, onset age, presence of AR, presence of asthma and presence of respiratory atopy (either AR or asthma) did not show statistically significant influence on disease course. Conclusions Children in Taiwan with early‐onset AD had disease of variable natural course, and the median disease duration was 4·2 years. About 70% of the patients went into remission eventually. The presence of AR or asthma did not affect the disease course of AD. What's already known about this topic? Atopic dermatitis (AD) commonly affects infants and children. The natural course of AD varies among individual patients. Spontaneous resolution occurs in some children as they grow older. What does this study add? The probability of children with early‐onset AD healing in a given time is calculated using nationwide population‐based data. About 70% of the patients with early‐onset AD went into remission eventually. Presence of allergic rhinitis or asthma did not affect the course of AD.