Simultaneous PET–MR acquisition provides the high temporal and spatial resolution of MRI with the specificity of PET. In PET, accurate modelling of physiological function in vivo requires the time-activity curve of tracer in blood plasma, known as the arterial input function (AIF). As the gold standard method of blood sampling is inherently prohibitive in the small animal case, here we discuss how we prepare to rapidly sample MRI signals from gadolinium-doped tracer to obtain the tracer input functions from a simultaneous PET-MR measurement. ΔR2⁎ measurements taken from EPI images were used to obtain first pass bolus AIFs in the rat brain from DSC-MRI datasets of 5 rats. AIFs obtained using our automatic algorithm were found to be consistent between animals and compared well with manual methods without need for a priori voxel selection. A variable flip angle FLASH sequence used for T1 mapping was successfully tested in a phantom study, providing accurate measurements of Gd concentration.