The condition of being underweight is a social problem in Japan among women. However, there is a lack of evidence for dietary guidance for underweight women because there has been no comparison of lipids or HbA1c among underweight, normal weight, and overweight women in different age groups. We analyzed the effect of body size and age on the serum lipid and hemoglobin A1c levels in Japanese women in a cross-sectional study. A total of 26,118 women aged >20-65 years underwent physical examinations between 2012 and 2022. Seventeen percent of women aged >20-29 years were underweight, and 8% of those aged 50-65 years were underweight. Total cholesterol and non-HDL-C concentrations increased with age, but the difference between underweight and overweight individuals was lowest among women aged 50-65 years. On the other hand, the differences in HDL-C, TG, and HbA1c levels between underweight and overweight subjects were greatest in the 50-65 age group, but the differences between underweight and normal weight subjects were much smaller. Considering that, unlike HDL-C, TG, and HbA1c, TC and non-HDL-C increase to levels comparable to overweight levels in underweight women in aged 50-65 years, educating people about a diet that lowers non-HDL-C is necessary even in young underweight women.