The introduction of the FD Rapid GolgiStain Kit has enabled many researchers to easily examine the morphology of neurons. Owing to an improved Golgi–Cox impregnation method, both stable and highly sensitive stained images of neurons can be acquired using this kit. To analyse microstructures such as dendritic spines and growth cones at detail, we attempted to create a useful method combining Golgi–Cox staining and electron microscopy (Golgi–EM method) so that the prepared Kit-stained samples would be appropriate for use in electron microscopy (EM) studies. Results from the present study suggest the importance of the glutaraldehyde fixation step in the Golgi–EM method. Here, we introduce the recommended protocol for the Golgi–EM method, which is available for ultrahigh-voltage electron microscopy and transmission electron microscopy. We are confident that our Golgi–EM method may become a reliable and important method that can contribute to new discoveries in neuronal morphology.