Yes.
Let $f\colon U \to X$ be an étale morphism. The absolute Frobenius $U \to U$, the absolute Frobenius $F \colon X \to X$, and the map $f\colon U \to X$ (twice) form a commutative square. This commutative square induces a morphism from $U$ to the fiber product of $U$ and $X$ over $X$ taken with respect to the maps $f$ and $F$, in other words to $F^{-1}(U)$. This morphism is natural and so gives a natural transform from the identity functor from the étale site of $X$ to itself to the absolute Frobenius from the étale site of $X$ to itself.
Because $f$ is étale, this commutative square is in fact Cartesian, so the induced morphism is an isomorphism, and the natural transformation is an isomorphism of functors.
Since $F^{-1}$ is isomorphic as a functor to the identity, their induced geometric morphisms on the topos of sheaves are equivalent.