The multiferroic ferrimagnet Cu$_2$OSeO$_3$ with a chiral crystal structure attracted a lot of recent attention due to the emergence of magnetic skyrmion order in this material. Here, the topological properties of its magnon excitations are systematically investigated by linear spin-wave theory and inelastic neutron scattering. When considering Heisenberg exchange interactions only, two degenerate Weyl magnon nodes with topological charges $pm$2 are observed at high-symmetry points. Each Weyl point splits into two as the symmetry of the system is further reduced by including into consideration the nearest-neighbor Dzyaloshinsky-Moriya interaction, crucial for obtaining an accurate fit to the experimental spin-wave spectrum. The predicted topological properties are verified by surface state and Chern number analysis. Additionally, we predict that a measurable thermal Hall conductivity can be associated with the emergence of the Weyl points, the position of which can be tuned by changing the crystal symmetry of the material.