This article presents a method to determine the magnetic field distribution within the vapor cell of a spin-exchange relaxation-free (SERF) atomic magnetometer with a sensitivity of the order of 10 femtoTesla and a bandwidth of DC to 100 Hz, in the presence of an uncompensated ambient magnetic field of up to several nanoTesla. The method is based on the analysis of the atomic polarization in a multichannel pump–probe configuration, in which a spatially selective optical pumping enables to probe specific layers of the atomic vapor contained in a gas-buffered cell. An SERF magnetometer is inherently sensitive to one component of the magnetic field, orthogonal to the pump and probe laser beams. The sensor’s performance can be drastically degraded by the other uncompensated components of the magnetic field. Typically, SERF magnetometry requires very good magnetic shielding and active compensation of residual magnetic field to properly function; this is commonly achieved by applying a complex design of Helmholtz coils in a sophisticated compensation procedure. The method suggested in this article eliminates the influence of non-uniform residual magnetic fields on the accuracy of measurements without precise compensation of the interfering field components. This procedure is used to simplify the measurements of magnetic field distribution in a large vapor cell with required accuracy. This is critically important for precise multichannel magnetic field mapping used for localization of the magnetic dipole-field source.