Effectiveness of exercise on bone mass is closely related to the mode of exercise training regimen, as well as the study design. This study aimed to determine the effect of different modes of exercise training on lumbar spine and femoral neck bone mineral density (BMD) in older postmenopausal women (PMW). PubMed, CINAHL, Medline, Google Scholar, and Scopus databases and reference lists of included studies were searched up until March 25, 2019 for randomized controlled trials (RCTs) that evaluated the effectiveness of various modes of exercise training in PMW. Sixteen RCTs with 1624 subjects were included. Our study found no significant change in both lumbar spine and femoral neck BMD following exercise training (MD:​ 0.01 g/cm²;​ 95% confidence interval (CI) [− 0.01, 0.02] and MD:​ 0.00 g/cm²;​ 95% CI [− 0.01, 0.01], respectively). However, subgroup analysis by type of exercise training revealed that lumbar spine BMD (MD:​ 0.01;​ 95% CI [0.00, 0.02]) raised significantly when whole-body vibration (WBV) was employed as intervention compared with RCTs that utilized aerobic (MD:​ − 0.01;​ 95% CI [− 0.02, − 0.01]), resistance (MD:​ 0.01;​ 95% CI [− 0.04, 0.06]), and combined training (MD:​ 0.03;​ 95% CI [− 0.01, 0.08]). On the other hand, lumbar spine BMD (MD:​ − 0.01;​ 95% CI [− 0.02, − 0.01]) reduced significantly when aerobic exercise training was used as intervention compared with RCTs that utilized resistance training, combined training, and WBV. By contrast, these analyses did not have significant effect on change in femoral neck BMD. WBV is an effective method to improve lumbar spine BMD in older PMW.