Bacterial exposure in infancy may be one of the determinants of atopic dermatitis (AD) morbidity in later life. Some clinical studies have shown that an intake of probiotics reduced the risks of AD in children; however, the timing and duration of administration for the prevention of AD still remain unclear. The aim of this study was to evaluate the effects on AD development of the administration of Lactobacillus johnsonii NC553 (La1) during the weaning period, using an animal model of human AD, NC/NgaTnd mice. La1 suspended in drinking water was administered to 4-week-old NC/NgaTnd mice for 4 weeks. Mice were kept up to 16 weeks of age in an air uncontrolled conventional condition. Clinical skin severity, scratching behaviour, histological features, and production of regulatory or inflammatory cytokines in spleens were analyzed. The results indicated that oral administration of La1 suppressed exacerbation of the clinical severity of dermatitis when compared to the controls. Scratching duration, which is the most important cause of skin damage, was also suppressed in mice fed with La1. La1 supplementation also suppressed epidermal hyperplasia and infiltration of inflammatory cells in skin. This study showed that exposure to La1 from the early stages might be beneficial to reduce the exacerbation of AD in children at high-risk of allergy.