The geophysical investigations through mobile multi-electrode system, like the Automatic Resistivity Profiling (ARP) method, can increase the size of the surveyed areas without jeopardizing the spatial resolution of the survey. The representation of the apparent resistivity data in maps corresponding to the different measuring dipoles is sufficient in most routine application in mapping the buried archaeological structures. In specific cases where a more quantitative interpretation of the apparent resistivity data is demanded, the three-dimensional (3-D) resistivity inversion can provide the necessary tool for this purpose. This work investigates the possibilities and limitations of the 3-D resistivity inversion in processing the ARP data. A 3-D finite element smoothness constrained inversion algorithm was used. The Active Constraint Balancing (ACB) method was also applied in order to enhance the stability and the resolving power of the inversion procedure. Resistivity models that are commonly encountered in archaeological exploration were used to generate synthetic apparent resistivity data using a 3-D finite element forward modelling program. Inversion of the synthetic data showed that the maximum investigation depth of the ARP method is comparable to length of the larger receiving dipole and can not exceed the 2-2.5 m for the ARP device tested in this work. Archaeological structures buried within this depth range can be effectively mapped, while the resolution of the subsurface structures is related to the data acquisition parameters. The processing of a relatively small data collected from Andilly archaeological site in France verified and enhanced the synthetic modeling results, showing that the 3-D inversion can act as a complementary tool in acquiring a more quantitative interpretation of the buried archaeological features.