Magnetoencephalography (MEG) measures neuromagnetic activity with high temporal, and theoretically, high spatial resolution. However, the ability of magnetic source imaging (MSI) to localize deep sources is uncertain. We developed an experimental platform combining MEG-compatible optogenetic techniques in non-human primates (NHPs) to test the ability of MEG/MSI to image deep signals. We demonstrate localization of optogenetically-evoked signals to known sources in the superficial arcuate sulcus of cortex and in CA3 of hippocampus at a resolution of 750 μm3. In response to stimulation of arcuate sulcus and hippocampus, we detected activation in subcortical and thalamic structures, or extended temporal networks, respectively. This is the first demonstration of accurate localization of deep sources within an intact brain using a novel combination of optogenetics with MEG/MSI. This approach is suitable for exploring causal relationships between discrete brain regions through precise optogenetic control and simultaneous whole brain recording.