We analyze the globular cluster (GC) systems in two very different galaxies, NGC3115 and NGC1399. With the papers of this series, we aim at highlighting common and different properties in the GC systems in galaxies covering a wide range of parameter space. We compare the GCs in NGC3115 and NGC1399 as derived from the analysis of one square degree u-, g -, and i-band images taken with the VST telescope as part of the VST early-type galaxy survey (VEGAS) and Fornax deep survey (FDS). We selected GC candidates using as reference the morpho-photometric and color properties of confirmed GCs. The surface density maps of GCs in NGC3115 reveal a morphology similar to the light profile of field stars; the same is true when blue and red GCs are taken separately. The GC maps for NGC1399 are richer in structure and confirm the existence of an intra-cluster GC component. We confirm the presence of a spatial off set in the NGC1399 GC centroid and find that the centroid of the GCs for NGC3115 coincides well with the galaxy center. Both GC systems show unambiguous color bimodality in (g - i) and (u - i); the color-color relations of the two GC systems are slightly different with NGC3115 appearing more linear than NGC1399. The azimuthal average of the radial density profiles in both galaxies reveals a larger spatial extent for the total GCs population with respect to the galaxy surface brightness profile. For both galaxies, the red GCs have radial density profiles compatible with the galaxy light profile, while the radial profiles for blue GCs are shallower. As for the specific frequency of GCs, S-N, we find it is a factor of two higher in NGC1399 than for NGC3115; this is mainly the result of extra blue GCs. By inspecting the radial behavior of the specific frequency, S-N(<r), for the total, blue, and red GCs, we find notable similarities between the trends for red GCs in the two targets. In spite of extremely different host environments, the red GCs in both cases appear closely linked to the light distribution of field stars. Blue GCs extend to larger galactocentric scales than red GCs, marking a significant difference between the two galaxies: the blue/red GCs and field stellar components of NGC3115 appear well thermalized with each other and the blue GCs in NGC1399 appear to fade into an unrelaxed intra-cluster GC population.