The estimation of the end-to-end delay in modern communication networks is of high importance to support multiple services but also for the management of the network resources. In this paper, we propose an end-to-end delay model and estimation methodology for heterogeneous networks. The estimation method allows the computation of the end-to-end delay distribution parameters when a small number of end-to-end delay samples is available through probe packets. The proposed technique is evaluated for different datasets, including networks operating with multiple access technologies and different upper-layer protocols, so the heterogeneity of the networks and protocols can be taken into account. The evaluation results show that the Generalized Extreme Value distribution can be used to approximate the end-to-end delay and high accuracy is achieved even when only a small number of probe packets is available. Finally, the estimation error confirms the effectiveness of the proposed method for a broad range of network scenarios.