Many glaciers in the Antarctic Peninsula are now rapidly losing mass. Understanding of the dynamics of these fast-flowing glaciers, and their potential future behaviour, can be improved through ice sheet modelling studies. Inverse methods are commonly used in ice sheet models to infer the spatial distribution of a basal friction coefficient, which has a large effect on the basal velocity and ice deformation. Here we use the full-Stokes Elmer/Ice model to simulate theWordie Ice Shelf-Fleming Glacier system in the southern Antarctic Peninsula. With an inverse method, we infer the pattern of the basal friction coefficient from surface velocities observed in 2008. We propose a multi-cycle spin-up scheme to reduce the influence of the assumed initial englacial temperature field on the final inversion. This is particularly important for glaciers like the Fleming Glacier, which have areas of strongly temperature-dependent deformational flow in the fast-flowing regions. Sensitivity tests using various bed elevation datasets, ice front positions and boundary conditions demonstrate the importance of high-accuracy ice thickness/bed geometry data and precise location of the ice front boundary.