An integral equation method for solving the Yukawa-Beltrami equation on a multiplyconnected sub-manifold of the unit sphere is presented. A fundamental solution for the YukawaBeltrami operator is constructed. This fundamental solution can be represented by conical functions. Using a suitable representation formula, a Fredholm equation of the second kind with a compact integral operator needs to be solved. The discretization of this integral equation leads to a linear system whose condition number is bounded independent of the size of the system. Several numerical examples exploring the properties of this integral equation are presented.