The effects of proton irradiation with energies of 3.5 and 5 MeV on the optical properties of PANDA (polarization-maintaining and absorption-reducing) optical fiber were investigated. The displacement and the ionization damage in the fiber induced by proton irradiation at 3.5, 5, and 10 MeV were calculated, respectively, using a Stopping and Range of Ions in Matter code. The irradiation-induced defects were analyzed by means of x-ray photoelectron spectroscopy, electron paramagnetic resonance, Fourier-transform infrared spectrometry, and broadband optical spectrum analysis. The results show that the proton irradiation leads to an increase of optical loss around 1310 nm and that the effect of 3.5 MeV protons is more severe than that of 5 MeV.