Background/Objectives: Chronic Kidney Disease–Mineral and Bone Disorder (CKD-MBD) is a frequent complication of chronic kidney disease, characterized by altered bone mineral density and mineral–hormonal metabolism. Therapeutic exercise may help attenuate these alterations, but evidence remains limited. This systematic review and meta-analysis evaluated the effects of therapeutic exercise on bone mineral density and mineral–bone and hormonal biomarkers in adults with CKD, focusing on CKD-MBD-related outcomes. Methods: Following a PROSPERO-registered protocol (CRD420251245021), Scopus, PubMed, Cochrane Central Register of Controlled Trials CENTRAL, and Web of Science were searched from inception to January 2026. Randomized controlled trials, including pilot randomized controlled trials, comparing therapeutic exercise with usual care or non-exercise control conditions in adults with CKD were included. Methodological quality and risk of bias were assessed with the PEDro scale and RoB 2, respectively. Results: Six studies involving 398 participants were included. Most interventions lasted 22 to 24 weeks and used resistance or combined aerobic and resistance exercise across inpatient and outpatient settings. Qualitative synthesis suggested improvements in femoral neck and lumbar spine bone mineral density and favorable biomarker changes. The assessed outcomes included femoral neck and lumbar spine BMD, calcium, phosphorus, sclerostin, PTH, FGF23, and klotho. Meta-analysis showed significant effects favoring therapeutic exercise for bone mineral density (MD = 0.05; 95% CI: 0.03 to 0.06; p < 0.00001; I² = 39%), mineral and bone-related biomarkers (SMD = 0.71; 95% CI: 0.42 to 0.99; p < 0.00001; I² = 75%), and hormonal biomarkers (SMD = 1.32; 95% CI: 0.88 to 1.77; p < 0.00001; I² = 85%). Conclusions: Therapeutic exercise may have beneficial effects on bone mineral density and selected mineral and hormonal biomarkers in adults with CKD. However, confidence in these findings is limited by the small number of studies, differences in CKD stage and exercise protocols, methodological limitations, risk of bias, and substantial heterogeneity in several pooled analyses. No definitive conclusions can currently be drawn regarding the optimal exercise modality, dose, or effects across CKD stages.