Pro-inflammatory milieu of chronic kidney disease (CKD) results in endothelial damage and contributes to increased cardiovascular risk. The aim of the study was to evaluate association between neutrophil-to-lymphocyte ratio (NLR) and plasma relative expression of endothelially abundant miR-126-3p with circadian blood pressure (BP) pattern in CKD patients. This single-center observational study involved CKD stage 1-5 patients and healthy age- and sex-matched control subjects. All study participants had 24-h automatic blood pressure measurement (ABPM) performed. Plasma miRNA was quantified by qRT-PCR, in relation to endogenous U6 snRNA. In total, 90 CKD patients (60 ± 14 years, 52% males, 33 renal transplant recipients) and 25 healthy control subjects (55 ± 13 years, 48% males, p > 0.05) were enrolled in the study. We observed a positive correlation between miR-126-3p and average nighttime SBP (rho = 0.27, P = 0.02), average nighttime DBP (rho = 0.32, P = 0.003), night-day SBP ratio (ND-SBP), rho = 0.23, P = 0.03 and night-day DBP ratio (ND-DBP), rho = 0.26, P = 0.02. A positive association was found between NLR and average nighttime SBP (rho = 0.25, P = 0.01), ND-SBP (rho = 0.26, P = 0.006), and ND-DBP (rho = 0.28, P = 0.03). In the multiple regression model, NLR remained an independent predictor of average nighttime SBP (Beta per log change of NLR [95% CI]: 11.2 [1.8-10.6], P = 0.02), whereas miR-126-3p of nighttime DBP (1.88 [0.48; 3.28], p = 0.009), The results of our study point towards a link between both NLR and miR-126-3p and nighttime hypertension in CKD patients.