This article presents a systematic analysis of the retention behavior of two proton pump inhibitors (pantoprazole and rabeprazole) on two homemade ZIC-HILIC stationary phases with different space chains between the ionic site groups (ZIC-HILIC1 and ZIC-HILIC4). The effect of varying spacer lengths on the retention behaviors of pantoprazole and rabeprazole was examined. Factors that impact the analyst's chromatographic performance, such as the organic modifier ratio, pH levels, and acetate buffer ionic strength, were examined. The chromatographic separation was carried out on two zwitterionic stationary phases (100 mm ×4.6 mm ID, 3.5µm) column. The mobile phase was composed of 80% acetonitrile and 20% acetate buffer (40 mM) at pH 4.75; the flow rate was 0.5 mL/min with isocratic elution, and the detection was carried out using a UV detector at 285nm. The linearity range for pantoprazole and rabeprazole were 0.05-10 μg.ml-1, 0.05-17μg.ml-1 respectively. LOD (0.025and0.015 µg. mL-1), LOQ (0.075 and 0.045 µg. mL-1) for pantoprazole in ZIC-HILIC1 and ZIC-HILIC4 respectively, LOD (0.008 and0.006 µg. mL-1), LOQ (0.024 and 0.0.018 µg. mL-1) for rabeprazole in ZIC-HILIC1 and ZIC-HILIC4 respectively. The mean percentage recoveries of pantoprazole and rabeprazole were found to be (98.60%-99.83%) and (98.50%-101.00%) respectively. This method has been used effectively to determine the pantoprazole and rabeprazole contents in pharmaceutical preparations.