Monitoring cortical responses to neuromodulation on preclinical models can elucidate fundamental mechanisms of brain function. Concurrent brain stimulation and imaging is challenging, usually compromising spatiotemporal resolution, accuracy, and versatility. Here, we report on a non-invasive brain stimulation system with electronic control of neuromodulation parameters in a 9.4-T magnetic resonance imaging (MRI) environment. In the imaging scanner, multi-coil transcranial magnetic stimulation (mTMS) is delivered with a 2-coil array, and the MRI signal is measured with a radiofrequency coil. The mTMS can change the stimulus orientation with 1° resolution in a millisecond. Without physically rotating the coils, we evoked orientation-specific muscle responses after cortical stimulation on an anesthetized rat. The mTMS system was successfully implemented and tested with the small-animal MRI, showing minimal interference with B 0 and B 1 + fields and uncompromised image quality. A delay of 40 ms between the stimulation pulse and fMRI acquisition—similar or even shorter than those previously described in humans—led to artifact-free images. Concurrent electronically targeted brain stimulation and neuroimaging provides a valuable tool for exploring whole-brain network functions, endorsing more efficient treatment protocols.