We present an analysis of the FUSE spectra of HD 163296, a young isolated Herbig Ae star. The spectra in the far UV spectral range are dominated by strong emission lines of C III and O VI, which exhibit broad and complex asymmetric profiles with wings extending over more than 1000 km s-1. The H I Ly alpha and the C III emission profiles show evidence for an outflow with a terminal velocity of 270 km s-1. We also identified several narrower emission lines due to fluorescent decays in Fe II. Using an HST/STIS archive spectrum, we checked that the H I Ly alpha line, which has a clear type III P Cygni emission profile, is broad enough to provide the photons required to photo-excite the Fe II upper levels. As previously explored for the well-known Herbig Ae star AB Aur, most of the spectral features including the fluorescent lines are consistent with the presence of a chromosphere above the photosphere. However, the over-ionized species cannot be produced in this region alone and we discuss two alternative mechanisms to explain such spectral signatures: magnetospheric accretion and a magnetically confined wind. Both interpretations involve a large-scale magnetic field whose detection is now a challenge for the new generation of spectropolarimeters such as ESPaDOnS.