For a positive integer $q$, a $k$-uniform hypergraph $X=(V,E)$ is $q$-complementary if there exists a permutation $\theta$ on $V$ such that the sets $E, E^{\theta}, E^{\theta^2},\ldots, E^{\theta^{q-1}}$ partition the set of $k$-subsets of $V$. The permutation $\theta$ is called a $q$-antimorphism of $X$. The well studied self-complementary uniform hypergraphs are 2-complementary. For an integer $n$ and a prime $p$, let $n_{(p)}=\max\{i:p^i \text{divides} n\}$. In this paper, we prove that a vertex-transitive $q$-complementary $k$-hypergraph of order $n$ exists if and only if $n^{n_{(p)}}\equiv 1 (\bmod q^{\ell+1})$ for every prime number $p$, in the case where $q$ is prime, $k = bq^\ell$ or $k=bq^{\ell}+1$ for a positive integer $b < k$, and $n\equiv 1(\bmod q^{\ell+1})$. We also find necessary conditions on the order of these structures when they are $t$-fold-transitive and $n\equiv t (\bmod q^{\ell+1})$, for $1\leq t < k$, in which case they correspond to large sets of isomorphic $t$-designs. Finally, we use group theoretic results due to Burnside and Zassenhaus to determine the complete group of automorphisms and $q$-antimorphisms of these hypergraphs in the case where they have prime order, and then use this information to write an algorithm to generate all of these objects. This work extends previous, analagous results for vertex-transitive self-complementary uniform hypergraphs due to Muzychuk, Potočnik, Šajna, and the author. These results also extend the previous work of Li and Praeger on decomposing the orbitals of a transitive permutation group.