After forming a trench extending through an insulator layer and an underlying top semiconductor portion that is comprised of a first semiconductor material and a dopant of a first conductivity type to define an emitter and a collector on opposite sides of the trench in the top semiconductor portion, an intrinsic base comprising a second semiconductor material having a bandgap less than a bandgap of the first semiconductor material and a dopant of a second conductivity type opposite the first conductivity type is formed in a lower portion the trench by selective epitaxial growth. The intrinsic base protrudes above the top semiconductor portion and is laterally surrounded by entire top semiconductor portion and a portion of the insulator layer. An extrinsic base is then formed on top of the intrinsic base to fill a remaining volume of the trench by a deposition process.