We investigate chiral zero modes and winding numbers at fixed points on $T^2/mathbb{Z}_N$ orbifolds. It is shown that the Atiyah-Singer index theorem for the chiral zero modes leads to a formula $n_+-n_-=(-V_++V_-)/2N$, where $n_{pm}$ are the numbers of the $pm$ chiral zero modes and $V_{pm}$ are the sums of the winding numbers at the fixed points on $T^2/mathbb{Z}_N$. This formula is complementary to our zero-mode counting formula on the magnetized orbifolds with non-zero flux background $M eq 0$, consistently with substituting $M = 0$ for the counting formula $n_+ - n_- = (2M - V_+ + V_-)/2N$.