In this paper, we study the Hankel edge ideals of graphs. We determine the minimal prime ideals of the Hankel edge ideal of labeled Hamiltonian and semi-Hamiltonian graphs, and we investigate radicality, being a complete intersection, almost complete intersection and set theoretic complete intersection for such graphs. We also consider the Hankel edge ideal of trees with a natural labeling, called rooted labeling. We characterize such trees whose Hankel edge ideal is a complete intersection, and moreover, we determine those whose initial ideal with respect to the reverse lexicographic order satisfies this property.