There's a difference between electric potential and electric potential energy. The potential energy is a single number, and tells you how much energy you need to construct the system starting from point charges that are infinitely far away. The potential is a function of space, and tells you how much energy you would need to bring a unit charge from infinity to a given spatial point, holding all the other charges fixed.
For an isolated charge, (ignoring the self-energy, that is the energy needed to make the charge in the first place), the potential energy is zero. Since there are no other charges around, no energy is needed to move this point charge from infinity.
However, the potential is not zero, in fact it is $kq/r$, where $k$ is Coulomb's constant, $q$ is the charge, and $r$ is the distance from a given spatial point to the point charge. The potential tells us how much energy we would need to give to another point charge with charge $Q=1\ {\rm C}$ (assuming we are working in SI units) to bring it from infinity to a given point in space, while holding the original point charged fixed.