Systemic administration of cholinergic antagonist scopolamine (SCO) is a widely used model to induce experimental cognitive impairment during preclinical drug testing of putative procognitive compounds. This model, however, has limited predictive validity partly due to its peripheral side-effects, therefore objective neuroimaging measures would greatly enhance its translational value. To this end, we administered SCO and peripherally acting butylscopolamine (BSCO) in preclinical functional MRI (fMRI, 9.4T) studies and measured their effects on whisker stimulation induced fMRI activation in Wistar rats. Beside the commonly used gradient echo echo-planar imaging (GE EPI) an arterial spin labeling method was also used to elucidate the vasculature-related properties of the BOLD-response. To account for anesthesia-effects, in two separate experiments we used isoflurane and combined (isoflurane + i.p. dexmedetomidine) anesthesia. In the second experiment with GE EPI and spin echo (SE) EPI sequences the effect of donepezil (DON) was also examined. In isoflurane anesthesia with GE EPI, SCO decreased the evoked BOLD response in the barrel cortex (BC), while BSCO increased it in the anterior cingulate cortex. In the combined anesthesia SCO decreased the activation in the BC as well as in the inferior colliculus (IC) while BSCO reduced the response merely in the IC. Our results revealed that SCO attenuated the evoked BOLD activation in the BC as a probable central effect in both experiments while its other detected actions depended on the type of anesthesia or dose and the given fMRI sequences.