Electric potential energy is stored by a system consisting of at least two charges.
Let the two charges have the labels $1$ and $2$.
The force on charge $1$ due to charge $2$ is $\vec F_{12}$ and the force on charge $2$ due to charge $1$ be $\vec F_{21}$
Newton's third law tells you that $\vec F_{12}=-\vec F_{21}$ so the magnitude of the forces in each of the charges is the same.
The usual next step is to say that the position of one of the charges is fixed so any eternal force acting on that charge does no work.
So if it is charge $2$ which is fixed in position the external force acting on it $-\vec F_{21}$ suffers no displacement and hence does no work.
Changing the position of charge $1$ relative to the fixed charge $2$ requires an external force $-\vec F_{12}$ to do work as there is a displacement of this force and the amount of work done by the external force is the change in the electric potential energy of the system of two charges.
The process could have been reversed with charge $1$ as the fixed charge and charge $2$ as the charge which is moved and if the charges started and finished at the same relative positions as when charge $1$ was moved then the work done and hence the change in electric potential energy be the same.