Amorphous silicon dioxide films arise naturally by exposure of silicon surfaces to atmospheric environments. When used as electrodes in Li-ion batteries, the characterization of surface lithiation is relevant to the understanding of the performance of Si anodes. In this work, density functional theory analyses of the lithiation of an amorphous silicon dioxide film reveal the lithiation mechanisms and the role of the surface functional groups on the lithiation reactions and on the structure of the lithiated film. The surface concentration of silanol groups and structure of the optimized model of amorphous hydroxylated silicon dioxide film agree with those observed experimentally. It is found that Li is incorporated via breaking of Si–O bonds and partial reduction of the Si atoms. Evaluation of the formation energy for lithiation of the film indicates that the film would saturate at a Li/Si ratio of 3.48. Analyses of radial distribution functions and coordination numbers show the evolution of the structure upon lithiation, indicating the presence of Li6O complexes stabilized by the surrounding Si atoms.