Cerebral Blood Flow (CBF) as measured with ASL-MRI is an emerging Alzheimer’s Disease (AD) biomarker. However, vascular pathology may delay the arterial transit time (ATT) of the magnetic label and influence the measurement. Thus, ATT estimation can potentially reveal vascular pathology and benefit CBF quantification. To evaluate CBF and ATT as read-out markers in AD mouse models, time-encoded ASL was used to measure ATT and CBF in the APPswe/PS1ΔE9 AD model. No major CBF difference was found when ATT was taken into account. However, AD mice showed increased ATT in the thalamus and decreased CBF in the cortex and striatum.