The magnetic structure and magnetic phase transitions of the Pr5Ge4 compound are investigated by means of neutron powder diffraction (NPD) and small-angle neutron scattering (SANS). Both NPD and SANS indicate the existence of two magnetic phase transitions at 25 K and 42 K. Refinement of the crystal structure based on the high-resolution NPD data shows that from room temperature to 1.6 K the compound maintains the Sm5Ge4-type structure (Pnma, Z=4), in which Ge atoms occupy two 4c sites and one 8d site and Pr atoms occupy two 8d sites and one 4c site. Refinements of the magnetic structures reveal that the two magnetic transitions essentially correspond to the long-range orderings of the Pr moments on different crystallographic sites. The Pr moments on the 4c site order ferromagnetically with Pn(')ma(') symmetry at 42 K and induce small ordered Pr moments on the 8d sites. The long-range ordering of the Pr moments on the 8d sites develops at 25 K with Pnm(')a(') symmetry. The separate ordering of the Pr moments on different crystallographic sites can be readily understood by the salient difference in the rare earth metal environments between the different crystallographic sites. The Pr moments on the 4c site in Pr5Ge4 compound align along the b axis, in contrast to other reported R5Ge4 compounds, and can be attributed to the contribution of higher-order terms of crystal-field to magnetocrystalline anisotropy of the various R atoms in the R5Ge4 compounds.