Objectives: Chronic kidney disease (CKD) poses challenges in pediatric patients, one of which is mineral and bone disorder (MBD), which leads to vascular calcification and accelerated atherosclerosis, compromising cardiovascular health. Carotid intima-media thickness (cIMT) is a measure of atherosclerotic vascular disease and a surrogate biomarker for cardiovascular risk in patients with CKD. Increased fibroblast growth factor 23 (FGF23)—the earliest detectable serum abnormality associated with CKD-MBD—has been linked with cardiovascular outcomes in patients with CKD. Our study aims to identify factors contributing to increased cIMT, FGF23, and suboptimal MBD control in pediatric CKD. Methods: We recruited 43 children (ages 2–18) with CKD stages 2 to 5D at Dr. Sardjito General Hospital, Indonesia. cIMT was measured using Philips HD15 echocardiography by a blinded examiner, including left ventricular mass index (LVMI). Blood samples were collected for FGF23 analysis, with additional assessment of other parameters associated with CKD-MBD, including hemoglobin, creatinine, albumin, uric acid, calcium, phosphate, and PTH levels. Statistical analyses were applied to examine associations among cIMT, FGF23, and MBD. Results: Higher FGF23 levels were significantly associated with the presence of MBD (r=0.83, p<0.001), lower eGFR (r=-0.49, p<0.001), advanced CKD (r=0.33, p<0.05), patients requiring dialysis (r=0.69, p<0.05), hypertension (r=0.24, p=0.02), and higher LVMI (r=0.51, p<0.001). No variable exhibited a significant correlation with cIMT measurements. Hemodialysis patients had poorer MBD parameters and higher FGF23 and cIMT than those on peritoneal dialysis, although the differences were insignificant. Conclusions: FGF23 levels increased with CKD progression and the presence of CKD-MBD. Elevated FGF23 may be associated with increased MBD prevalence in late-stage CKD. The relationships between cIMT with FGF23, MBD, and cardiovascular outcomes in CKD have not been conclusively demonstrated in our study. A more extensive study is needed to validate the factors affecting cIMT in children with CKD.