Chronic kidney disease (CKD) is associated with increased fracture risk and skeletal deformities. The impact of CKD on volumetric bone mineral density (BMD) and cortical dimensions during growth is unknown. Tibia quantitative computed tomography scans were obtained in 156 children with CKD [69 stage 2–3, 51 stage 4–5, and 36 stage 5D (dialysis)] and 831 healthy participants, ages 5–21 years. Sex-, race-, and age- or tibia length-specific Z-scores were generated for trabecular BMD (TrabBMD), cortical BMD (CortBMD), cortical area (CortArea) and endosteal circumference (EndoC). Greater CKD severity was associated with higher TrabBMD-Z in younger participants (p < 0.001), compared with healthy children; this association was attenuated in older participants (interaction p < 0.001). Mean CortArea-Z was lower (p < 0.01) in CKD 4–5 [−0.49 (95% C.I. −0.80, −0.18)] and 5D [−0.49 (−0.83, −0.15)], compared with healthy children. Among CKD participants, parathyroid hormone (PTH) levels were positively associated with TrabBMD-Z (p < 0.01), and this association was significantly attenuated in older participants (interaction p < 0.05). Higher levels of PTH and biomarkers of bone formation (bone-specific alkaline phosphatase) and resorption (β-CTX) were associated with lower CortBMD-Z and CortArea-Z, and greater EndoC-Z (r = 0.18–0.36; all p ≤ 0.02). CortBMD-Z was significantly lower in CKD participants with PTH levels above vs. below the upper limit of the KDOQI CKD stage-specific target range: −0.46 ± 1.29 vs. 0.12 ± 1.14, p < 0.01. In summary, childhood CKD and secondary hyperparathyroidism were associated with significant reductions in cortical area and CortBMD, and greater TrabBMD in younger children. Future studies are needed to establish the fracture implications of these alterations and to determine if cortical and trabecular abnormalities are reversible.