We give an error estimate for the energy and helicity preserving scheme (EHPS) in second order finite difference setting on axisymmetric incompressible flows with swirling velocity. This is accomplished by a weighted energy estimate, along with careful and nonstandard local truncation error analysis near the geometric singularity and a far field decay estimate for the stream function. A key ingredient in our a priori estimate is the permutation identities associated with the Jacobians, which are also a unique feature that distinguishes EHPS from standard finite difference schemes.