By combining two independent approaches, inelastic neutron scattering measurements and density functional theory calculations, we study the spin-waves in the high-temperature collinear antiferromagnetic phase (AFM2) of Mn$_5$Si$_3$. We obtain its magnetic ground-state properties and electronic structure. This study allowed us to determine the dominant magnetic exchange interactions and magnetocrystalline anisotropy in the AFM2 phase of Mn$_5$Si$_3$. Moreover, the evolution of the spin excitation spectrum is investigated under the influence of an external magnetic field perpendicular to the anisotropy easy-axis. The low energy magnon modes show a different magnetic field dependence which is a direct consequence of their different precessional nature. Finally, possible effects related to the Dzyaloshinskii-Moriya interaction are also considered.