Benidipine and amlodipine are two well-known drugs used in hypertensive patients with chronic kidney disease (CKD). In this systematic review we aimed to compare benidipine and amlodipine in terms of efficacy in the management of hypertensive patients. We searched PubMed, Cochrane CENTRAL, SCOPUS and Web of Science for relevant clinical trials and excluded observational studies. Quality appraisal was evaluated according to GRADE and we assessed the risk of bias using the Cochrane’s risk of bias tool. We included the following outcomes: Systolic blood pressure, diastolic blood pressure, heart rate, estimated glomerular filtration rate (eGFR), and urinary albumin/creatinine ratio. Data were pooled as mean differences (MD) with relative 95% confidence intervals (CI). Eight studies were eligible for our meta-analysis. We found no significant difference between both drugs regarding systolic (MD = − 0.21 [− 1.48, 1.89], (P = 0.81) and diastolic (MD = 0.01[− 0.51, 0.53], (P = 0.97)) blood pressure measurements. The overall heart rate did not differ as well (MD = − 0.03 [− 1.63, 1.57], (P = 0.97)). We found that benidipine was statistically better than amlodipine in terms of eGFR (MD = 1.07 [0.43, 1.71], (P = 0.001)), and urinary albumin/creatinine ratio (MD = − 43.41 [− 53.53, − 33.29], (P