Provided is a method of fabricating a heterojunction bipolar transistor (HBT). The method includes: sequentially depositing a sub-collector layer, a collector layer, a base layer, an emitter layer, and an emitter capping layer on a substrate; forming an emitter electrode on the emitter capping layer; forming a mesa type emitter to expose the base layer by sequentially etching the emitter capping layer and the emitter layer using the emitter electrode as an etch mask in vertical and negative-sloped directions to the substrate, respectively; and forming a base electrode on the exposed base layer using the emitter electrode as a mask in self-alignment with the emitter electrode. In this method, a distance between the mesa type emitter and the base electrode can be minimized and reproducibly controlled. Also, a self-aligned device with an excellent high-frequency characteristic can be embodied.