We study fermionic zero modes in the self-dual vortex background on an extra two-dimensional Riemann surface in 5+1 dimensions. Using the generalized Abelian Higgs model, we obtain the inner topological structure of the self-dual vortex and establish the exact self-duality equation with topological term. Then we analyze the Dirac operator on an extra sphere and the effective Lagrangian of four-dimensional fermions with the self-dual vortex background. Solving the Dirac equation, the fermionic zero modes on a sphere in two simple cases are obtained.