We obtain two-sided estimates for the heat kernel (or the fundamental function) associated with the following fractional Schrödinger operator with negative Hardy potential $$Δ^{α/2} -λ|x|^{-α}$$ on $\RR^d$, where $α\in(0,d\wedge 2)$ and $λ>0$. The proof is purely analytical but elementary. In particular, for upper bounds of heat kernel we use the Chapman-Kolmogorov equation and adopt self-improving argument.