We present a semi-analytic model for the shear two-point correlation function of a cosmic shear survey with non-uniform depth. Ground-based surveys are subject to depth variations that primarily arise through varying atmospheric conditions. For a survey like the Kilo-Degree Survey (KiDS), we find that the measured depth variation increases the amplitude of the observed shear correlation function at the level of a few percent out to degree-scales, relative to the assumed uniform-depth case. The impact on the inferred cosmological parameters is shown to be insignificant for a KiDS-like survey. For next-generation cosmic shear experiments, however, we conclude that variable depth should be accounted for.