Pharmacological magnetic resonance imaging (phMRI) offers the potential to provide novel insights into the functioning of neurotransmitter systems and drug action in the central nervous system. To date, much of the neuropharmacological research that has applied phMRI techniques has focused on the dopaminergic system with relatively few studies into serotonergic function. In this article, we discuss the current capabilities of, and future potential for phMRI to address fundamental questions in serotonergic research using animal models. Firstly we review existing literature on the application of phMRI to the serotonergic system by exploring 3 broad research themes: (i) the functional anatomy of the serotonergic system; (ii) drug–receptor targeting and distribution; and (iii) disease models and drug development. Subsequently, we discuss the interpretation of phMRI data in terms of neuropharmacological action with a focus on issues specific to neuroimaging studies of the serotonergic system. Unlike other neuroimaging approaches such as positron emission tomography, phMRI methods do not currently offer sensitivity to markers of specific pharmacological action. However, they can provide in vivo markers of the neuropharmacological modulation of neuronal activity across the whole brain with unparalleled spatial and temporal resolution. Furthermore, due to the non-invasive nature of MRI, these markers are readily translatable to human studies. Whilst there are a number of constraints and limitations to phMRI methods that necessitate careful data interpretation, we argue that phMRI could become a valuable research tool in neuropharmacological studies of the serotonergic system.