We describe the embedded resolution of an irreducible quasi-ordinary surface singularity $(V,p)$ which results from applying the canonical resolution of Bierstone-Milman to $(V,p)$. We show that this process depends solely on the characteristic pairs of $(V,p)$, as predicted by Lipman. We describe the process explicitly enough that a resolution graph for $f$ could in principle be obtained by computer using only the characteristic pairs.