Objectives: This study aims to investigate the association between skeletal muscle mass index (SMI) and physical activity among female university students who had exercise habituation in junior and high school. Methods: The body composition of 120 Japanese female students was measured using the bioelectrical impedance analysis (BIA) method, and their physical activity level (PAL) was measured using a factorial method. Based on the ‘Dietary Reference Intakes for Japanese’ (DRIs-J), according to the Ministry of Health, Labour and Welfare, PAL (24-h energy consumption/basal metabolic rate) classifications were defined as low-PAL (PAL < 1.6), moderate-PAL (1.6 ≤ PAL < 1.9), and high-PAL (1.9 ≤ PAL < 2.2), respectively. Results: Individuals with low-PAL had a significantly lower SMI, especially for the lower limb muscles, than individuals with moderate-PAL or higher. More than 50% of the individuals with currently low-PAL corresponded or tended to correspond to the SMI cut-off value defined by the Asian Working Group for Sarcopenia or the 2017 National Health and Nutrition Survey of Japan. Therefore, more than half of the female students with currently low-PAL, even those with an exercise habituation in the past, corresponded to the cut-off value for muscle loss in sarcopenia diagnosis, particularly in the lower limbs. Conclusions These results suggest that it is important to maintain a moderate or higher level of physical activity in the DRIs-J classification, even for young women who used to exercise in the past, to maintain muscle mass accordingly.