We present the first far-UV spectra of the Herbig Be star HD 100546, observed by the Far Ultraviolet Spectroscopic Explorer (FUSE) as part of the Circumstellar Disks team program. We identified and analyzed numerous narrow absorption lines of circumstellar origin. Intense, broad and fairly asymmetric emission lines of $\ion{C}{ii}$, $\ion{C}{iii}$, $\ion{O}{vi}$ and $\ion{S}{ii}$ were also detected, spanning temperatures up to $3\times 10^5$ K. Comparison of the spectra recorded two years apart reveals strong spectral variations, not only in the emission lines but also in the circumstellar lines of $\ion{N}{i}$, $\ion{N}{ii}$, $\ion{O}{i}$, $\ion{Ar}{i}$ and $\ion{Fe}{ii}$. The varying absorption lines of $\ion{N}{i}$ and $\ion{O}{i}$ exhibit the largest velocity width, from $-200$ to +320 km s$^{-1}$, relative to the star's rest-frame. Variations on a timescale of an hour occurred only in the $\ion{N}{i}$ resonance triplet and $\ion{O}{i}$ ($^1$D) lines. The spectroscopic variability highlighted by these two observations and the line profile analysis reveal signatures of both outflow and infall processes, which appear to be related in this system. We suggest that these spectral signatures originate in a stellar magnetosphere, which likely interacts with the innermost part of the star's circumstellar disk. This interpretation can account for the main features observed in the spectrum of HD 100546: variable emission and absorption lines as well as suspected continuum variation.