Brain perfusion allows for the evaluation of cerebral hemodynamics, particularly in brain infarcts and tumors. Computed tomography (CT) perfusion (CTP) provides reliable data; however, it has a limited scan field of view and radiation exposure. Magnetic resonance (MR) perfusion provides detailed imaging of small structures and a wide scan field of view. However, no study has compared CTP and MR perfusion and assessed the correlation between the perfusion parameters measured using CTP and MR perfusion. The aim of the present study was to assess the correlation and agreement of the cerebral perfusion derived from dynamic susceptibility contrast (DSC)-MRI and CTP in dogs. In this crossover design study, the cerebral blood volume (CBV), cerebral blood flow (CBF), mean transit time, and time to peak were measured in the temporal cerebral cortex, caudate nucleus, thalamus, piriform lobe, and hippocampus using CTP and DSC-MRI in six healthy beagle dogs and a dog with a pituitary tumor. On the color map of healthy beagles, blood vessels and the perivascular brain parenchyma appeared as red-green, indicating high perfusion, and the areas distant from the vessels appeared as green-blue, indicating low perfusion levels in CTP and DSC-MRI. CTP parameters were highest in the piriform lobe (CBF = 121.11 ± 12.78 mL/100 g/min and CBV = 8.70 ± 2.04 mL/100 g) and lowest in the thalamus (CBF = 63.75 ± 25.24 mL/100 g/min and CBV = 4.02 ± 0.55 mL/100 g). DSC-MRI parameters were also highest in the piriform lobe (CBF = 102.31 ± 14.73 mL/100 g/min and CBV = 3.17 ± 1.23 mL/100 g) and lowest in the thalamus (CBF = 37.73 ± 25.11 mL/100 g/min and CBV = 0.81 ± 0.44 mL/100 g) although there was no statistical correlation in the quantitative perfusion parameters between CTP and DSC-MRI. In a dog with a pituitary tumor, the color map of the tumor appeared as a red scale, indicating high perfusion and higher CBF and CBV on CTP (149 mL/100 g and 20 mL/100 g/min) and on DSC-MRI (116.3 mL/100 g and 15.32 mL/100 g/min) compared to those measured in healthy dogs. These findings indicate that DSC-MRI and CTP maps exhibit comparability and interchangeability in the assessment of canine brain perfusion.