Background The high prevalence of underweight in young women has become a serious health problem in Japan. When and how young women reach a low body mass index (BMI) has not been clarified. Aim To clarify the characteristics of BMI standard deviation scores (BMI SDS) trajectory of young Japanese women with underweight. Subjects and methods A total of 601 Japanese female university students aged 20 years were classified into underweight and healthy weight groups. Their school health check-up data were available from the ages of 6 to 20 years. We evaluated the estimated mean values of BMI SDS at each age and differences in BMI SDS (ΔBMI SDS) from 6 years to each age using a mixed-effects model and compared between the two groups at each age. Results In the underweight group, the BMI SDS at every age (−1.67 to −0.91) and the ΔBMI SDS after 16 years of age (−0.76 to −0.38) were significantly lower than those in the healthy weight group (−0.41 to −0.13, −0.07 to 0.04), respectively. Conclusion Young Japanese women with underweight have at least two characteristics of BMI SDS trajectory: being constitutionally underweight and shifting their weight status from baseline towards underweight in their late teens.