Emerging evidence demonstrates an opportunity for using probiotics to support bone health, but findings in humans are limited. This systematic review investigated if probiotic supplementation improves bone mineral density (BMD) and bone structure in rodent models compared to no supplementation. Studies (n = 71) examining the effect of oral consumption of any probiotic strain on BMD or bone structure in rodents were included. Meta-analyses were conducted separately by study model (intact, ovariectomized) and bone site (femur, tibia, spine) to determine the probiotic effect (standardized mean difference, SMD) on volumetric BMD (vBMD), bone volume fraction (BV/TV), and cortical thickness (Ct.Th). Reasons for heterogeneity were explored (probiotic genus, sex, type of rodent). In intact rodents, probiotics resulted in greater vBMD (SMD = 0.43, 95% CI [0.13, 0.74], I2 = 3%, p < 0.05) and higher BV/TV (SMD = 0.63, 95% CI [0.25, 1.02], I2 = 57%, p < 0.05) at the femur without changes in cortical bone structure. In ovariectomized models, probiotic supplementation resulted in greater vBMD (femur: SMD = 1.28, 95% CI [1.01, 1.55], I2 = 3%, p < 0.05; tibia: SMD = 1.29, 95% CI [0.52, 2.05], I2 = 67%, p < 0.05; and spine: SMD = 1.47, 95% CI [0.97, 1.97], I2 = 26%, p < 0.05) as well as higher BV/TV (femur: SMD = 1.16, 95% CI [0.80, 1.52], I2 = 56%, p < 0.05; tibia: SMD = 2.13, 95% CI [1.09, 3.17], I2 = 79%, p < 0.05; spine: SMD = 2.04, 95% CI [1.17, 2.90], I2 = 76%, p < 0.05) and Ct.Th at the tibia (SMD = 2.35; 95% CI [0.72, 3.97], I2 = 82%, p < .0.05) but not at the femur versus control. The syntheses support probiotics as a strategy to improve bone outcomes in rodent models.