This chapter discusses challenges and practical approaches to animal fMRI with respect to anesthetic regimens, conscious animal studies, activation paradigms, optimal pulse sequence selection, and the rigor required for drug discovery applications. Examples on the use of animal fMRI to support drug discovery are presented. The examples illustrate (1) technical development and qualification of a quantitative assay for pain, (2) the use of pharmacological tools to support a link between a receptor antagonist elicited ASL-CBF change with the corresponding neuronal activity, and (3) interrogation of mechanism of action of an analgesic.