The goal of NASA’s Europa Clipper Mission is to investigate the habitability of the subsurface ocean within the Jovian moon Europa using a suite of ten investigations. The Europa Clipper Magnetometer (ECM) and Plasma Instrument for Magnetic Sounding (PIMS) investigations will be used in unison to characterize the thickness and electrical conductivity of Europa’s subsurface ocean and the thickness of the ice shell by sensing the induced magnetic field, driven by the strong time-varying magnetic field of the Jovian environment. However, these measurements will be obscured by the magnetic field originating from the Europa Clipper spacecraft. In this work, a magnetic field model of the Europa Clipper spacecraft is presented, characterized with over 260 individual magnetic sources comprising various ferromagnetic and soft-magnetic materials, compensation magnets, solenoids, and dynamic electrical currents flowing within the spacecraft. This model is used to evaluate the magnetic field at arbitrary points around the spacecraft, notably at the locations of the three fluxgate magnetometer sensors and four Faraday cups which make up ECM and PIMS, respectively. The model is also used to evaluate the magnetic field uncertainty at these locations via a Monte Carlo approach. Furthermore, both linear and non-linear gradiometry fitting methods are presented to demonstrate the ability to reliably disentangle the spacecraft field from the ambient using an array of three fluxgate magnetometer sensors mounted along an 8.5-meter (m) long boom. The method is also shown to be useful for optimizing the locations of the magnetometer sensors along the boom. Finally, we illustrate how the model can be used to visualize the magnetic field lines of the spacecraft, thus providing very insightful information for each investigation.Supplementary InformationThe online version contains supplementary material available at 10.1007/s11214-023-00974-y.