We present a solution to the Conjugacy Problem in the group of outer-automorphisms of $F_3$, a free group of rank 3. We distinguish according to several computable invariants, such as irreducibility, subgroups of polynomial growth, and subgroups carrying the attracting lamination. We establish, by considerations on train tracks, that the conjugacy problem is decidable for the outer-automorphisms of $F_3$ that preserve a given rank 2 free factor. Then we establish, by consideration on mapping tori, that it is decidable for outer-automorphisms of $F_3$ whose maximal polynomial growth subgroups are cyclic. This covers all the cases left by the state of the art.