Axial charge separation in small diameter, partially strained silicon nanowires is predicted from ab initio calculations with electrons and holes located in different ends of the wires. We show that this effect can be understood from the topologies of near-gap wave functions, and that it is enhanced by quantum confinement. The possibility of utilizing partial strain for charge separation at the nanoscale opens up a new avenue for designing solar cells by morphology control, where effectively a type-II homojunction is formed and charge separation is facilitated by thermalization.