A Quantum Field Theory is defined by its interaction Hamiltonian, and linked to experimental data by the scattering matrix. The scattering matrix is calculated as a perturbative series, and represented succinctly as a first order differential equation in time. Neural Differential Equations (NDEs) learn the time derivative of a residual network's hidden state, and have proven efficacy in learning differential equations with physical constraints. Hence using an NDE to learn particle scattering matrices presents a possible experiment-theory phenomenological connection. In this paper, NDE models are used to learn $\phi^4$ theory, Scalar-Yukawa theory and Scalar Quantum Electrodynamics. A new NDE architecture is also introduced, the Fourier Neural Differential Equation (FNDE), which combines NDE integration and Fourier network convolution. The FNDE model demonstrates better generalisability than the non-integrated equivalent FNO model. It is also shown that by training on scattering data, the interaction Hamiltonian of a theory can be extracted from network parameters.