Hyper-entanglement between two or more photonic degrees of freedom (DOF) can enhance and enable new quantum protocols by allowing each DOF to perform the task it is optimally suited for. Here we demonstrate the generation of photon pairs hyper-entangled between pulse modes and frequency bins. The pulse modes are generated via parametric downconversion in a domain-engineered crystal and subsequently entangled to two frequency bins via a spectral mapping technique. The resulting hyper-entangled state is characterized and verified via measurement of its joint spectral intensity and non-classical two-photon interference patterns from which we infer its spectral phase. The protocol combines the robustness to loss, intrinsic high dimensionality and compatibility with standard fiber-optic networks of the energy-time DOF with the ability of hyper-entanglement to increase the capacity and efficiency of the quantum channel, already exploited in recent experimental applications in both quantum information and quantum computation.