Learning information and making flexible, appropriate choices are essential in everyday life. Animal model studies indicate the mediodorsal thalamus (MD) plays an important role in learning and decision-making. It is proposed to be an active partner supporting communication between the frontal and medial temporal lobes and other subcortical structures. To understand the contribution of each brain structure, it is critical we know its function and its anatomical connectivity. The latter helps inform which cortical and subcortical structures interact and how information travels throughout the brain. We investigated what brain structures showed activation at the whole brain level when combining electrical microstimulation of either the magnocellular (MDmc) or parvocellular subdivision of MD with functional magnetic resonance imaging (fMRI) in three anaesthetized male adult rhesus macaques. The neuroimaging scans demonstrated that microstimulation applied to the MD elicited increased as well as decreased fMRI activations in several cortical (anterior cingulate cortex, dorsolateral and ventrolateral prefrontal cortex, insular cortex, and orbitofrontal cortex) and subcortical (caudate, VTA, midbrain and brainstem) areas. These areas all have known MD anatomical connections. Some of the strongest activations were observed in the dorsal anterior cingulate cortex. Interestingly, each monkeys’ heart rate substantially increased during MD microstimulation, in particular when applied to the MDmc, highlighting the additional contribution of the MD to physiological, as well as cognitive functions. fMRI combined with microstimulation can be used to investigate connectivity at the whole brain level. Importantly though, more detailed histological investigations remain necessary to investigate the nature of these connections.