Osteoporosis is a prevalent disease that is associated with increased hip fractures which cause significant decline in quality of life. Tooth loss affects systemic condition such as cognitive function through various mechanism, but the link between tooth loss and femoral bone mineral density is still uncertain. This study aims to investigate whether tooth loss in young mice affects memory function and femoral bone mineral density. Eight-week-old male C57BL/6 J mice were allocated randomly into the control group with sham operation and the tooth-loss group extracted all maxillary molar. Step-through passive avoidance test as cognitive function test, micro-CT analysis and western blotting analysis were performed after 1- and 2-month observation period. Step-through passive avoidance test revealed that the tooth-loss group in 2-month observation period impaired cognitive function. Additionally, micro-CT analysis revealed a significant decrease in both the length of the mandible and bone mineral density in the femur of the tooth-loss group compared to the control group. Claudin-5 level in the hippocampus, which is one of the tight junction markers in blood–brain-barrier, was significantly decreased in the tooth-loss group. The findings of our present study suggested that tooth loss impair cognitive function accompanied by reduced tight-junction marker, mandibular growth and bone mineral density of femur.