I know that we can find two subgroups of $\mathfrak{S}_6$ both isomorphic to $\mathfrak{S}_5$ that are however not conjugate (here) in $\mathfrak{S}_6$. These subgroups are not conjugate precisely because one and only one of them is transitive.
Can we find two transitive subgroups of a symetric group that are isomorphic but not conjugate ?