Cerebrovascular reactivity (CVR) is an important marker of the brain’s vascular health. BOLD MRI with hypercapnia challenge has been shown to be a promising method to measure CVR in various cerebrovascular conditions. To prepare this method for larger-scale multi-site studies, a cross-vendor comparison was performed to evaluate the variability of this CVR mapping method across different scanner platforms. CVR, bolus arrival time and functional connectivity networks were found to be measured reliably from both Philips and Siemens 3T scanners using this method. Although CVR was highly correlated between the two scanners, there was slight difference in CVR values between them.