Immunoglobulin superfamily member 9b (IgSF9b) is a cell adhesion protein that has been linked to the etiology of several psychiatric disorders, including bipolar disorder and schizophrenia. Based on previous studies in neuronal cultures, IgSF9b was proposed to specifically regulate the structure and function of GABAergic synapses in the brain through an indirect interaction with the synaptic adhesion protein Neuroligin-2. To date, however, very little is known about the expression pattern of IgSF9b in the intact brain, and the synaptic localization of IgSF9b in different brain regions has never been investigated. To address this question, we conducted an immunohistochemical characterization of IgSF9b expression across the mouse brain and investigated its colocalization with gephyrin, Neuroligin-2 and VIAAT as markers of GABAergic synapses, as well as with PSD-95 and vGlut1 as markers of glutamatergic synapses. Unexpectedly, we observed that in the majority of brain regions assessed, only a small fraction of IgSF9b puncta colocalized with GABAergic synapses, with a similarly small fraction colocalizing with glutamatergic synapses. The majority of IgSF9b puncta were not associated with any of the investigated synaptic markers, indicating that IgSF9b plays an additional non-synaptic role. Accordingly, deletion of IgSF9b resulted in only subtle alterations in markers of GABAergic synapses, most prominently a reduction in the size of gephyrin and Neuroligin-2 puncta in the lateral habenula, which plays a key role in the regulation of affective behaviors. Together, our findings provide an important context for the assessment of the role of IgSF9b in psychiatric disorders.