The efficient simulation of correlated quantum systems is a promising near-term application of quantum computers. Here, we present a measurement of the second Renyi entropy of the ground state of the two-site Fermi-Hubbard model on a five-qubit programmable quantum computer based on trapped ions. Our work illustrates the extraction of a nonlinear characteristic of a quantum state using a controlled-swap gate acting on two copies of the state. This scalable measurement of entanglement on a universal quantum computer will, with more qubits, provide insights into many-body quantum systems that are impossible to simulate on classical computers.