As a prevention, a physically active lifestyle including the performance of weight-bearing exercises is important to enhance and maintain bone mineral content. Fifty young women were selected for the study. Twenty-five women carried out a specific training directed by a physiotherapist in the training group (TG), while 25 women were walking for 60 minutes in the control group (CG). Total and bone-specific alkaline phosphatase (ALP and BALP) and C-terminal cross-linked telopeptide (CTX) levels were measured at the beginning and at the end of exercise. The most remarkable change was seen in CTX levels (TG -28.89%, p < 0.001; CG -52.54%, p < 0.001), and there was also a significant difference in the values of CTX between TG and CG (p = 0.012). Therefore, walking more significantly reduced the level of CTX than special exercise. The decrease of BALP in TG was considerable but not significant (TG -4.63%, p = 0.091), while BALP levels dropped significantly in CG (-7.65%, p = 0.011), and there was a non-significant difference between the two groups (p = 0.22). Regarding the ALP level, a significant reduction was detected in TG and CG (-6.84%, p < 0.001 vs. -4.57%, p < 0.001). This study reveals that the 60-minute, middle-intensity training and the brisk walking have an immediate effect on bone metabolic markers.