Three-dimensional van der Waals ferromagnet Fe3GeTe2 (FGT) is regarded as a candidate for the magnetic topological nodal line semimetal. We investigate lateral electron transport between two 3 µm spaced superconducting In leads beneath a thick three-dimensional FGT exfoliated flake. At low 30 mK temperature, we observe Josephson supercurrent that exhibits unusual critical current Ic suppression by the magnetic field B. The overall Ic(B) pattern is asymmetric in respect to the B sign. We demonstrate, that the asymmetry is defined by the magnetic field sweep direction, so the Ic(B) pattern is strictly reversed (as B to −B inversion) for the opposite sweeps. We also observe an interplay between maximum and minimum in Ic(B) in normal magnetic fields, while there are fast aperiodic Ic(B) fluctuations for the in-plane ones. These effects can not be expected for homogeneous superconductor-ferromagnet-superconductor junctions, while they are known for Josephson spin valves. The mostly possible scenario for Josephson spin valve realization in FGT is the misalignment of spin polarizations of the Fermi arc surface states and ferromagnetic FGT bulk, but we also discuss possible influence of spin-dependent transport between magnetic domains.