In the reaction-diffusion process $A+B to varnothing$ on random scale-free (SF) networks with the degree exponent $gamma$, the particle density decays with time in a power law with an exponent $alpha$ when initial densities of each species are the same. The exponent $alpha$ is $alpha > 1$ for $2 < gamma < 3$ and $alpha=1$ for $gamma ge 3$. Here, we examine the reaction process on fractal SF networks, finding that $alpha < 1$ even for $2 < gamma < 3$. This slowly decaying behavior originates from the segregation effect: Fractal SF networks contain local hubs, which are repulsive to each other. Those hubs attract particles and accelerate the reaction, and then create domains containing the same species of particles. It follows that the reaction takes place at the non-hub boundaries between those domains and thus the particle density decays slowly. Since many real SF networks are fractal, the segregation effect has to be taken into account in the reaction kinetics among heterogeneous particles.