Assessing cardiovascular disease (CVD) in children with chronic kidney disease (CKD) is difficult. Great expectations have been associated with biomarkers, including the N-terminal pro-brain natriuretic peptide (NT-proBNP). This study aimed to determine the correlation between NT-proBNP and cardiovascular complications in children with CKD. Serum NT-proBNP, arterial stiffness, common carotid artery intima-media thickness (cIMT), echocardiographic (ECHO) parameters (including tissue Doppler imaging), and biochemical and clinical data were analyzed in 38 pediatric patients with CKD (21 boys, 12.2 ± 4.2 years). Mean NT-proBNP in CKD patients was 1068.1 ± 4630 pg/mL. NT-proBNP above the norm (125 pg/mL) was found in 16 (42.1%) subjects. NT-proBNP correlated with glomerular filtration rate (GFR) (r = −0.423, p = 0.008), and was significantly higher in CKD G5 (glomerular filtration rate grade) patients compared to CKD G2, G3, and G4 children (p = 0.010, p = 0.004, and p = 0.018, respectively). Moreover, NT-proBNP correlated positively with augmentation index (AP/PP: r = 0.451, p = 0.018, P2/P: r = 0.460, p = 0.016), cIMT (r = 0.504, p = 0.020), and E/E’ in ECHO (r = 0.400, p = 0.032). In multivariate analysis, logNT-proBNP was the only significant predictor of cIMT Z-score (beta = 0.402, 95CI (0.082–0.721), p = 0.014) and P2/P1 (beta = 0.130, 95CI (0.082–0.721), p = 0.014). Conclusions: NT-proBNP may serve as a possible marker of thickening of the carotid artery wall in pediatric patients with CKD. The final role of NT-proBNP as a biomarker of arterial damage, left ventricular hypertrophy, or cardiac diastolic dysfunction in CKD children needs confirmation in prospective studies.