This study aimed to investigate the effects of different femtosecond (fs) laser treatment protocols on the surface roughness (Ra) and shear bond strength (SBS) of resin cement to zirconia. A total of 110 zirconia specimens were divided into 11 subgroups according to the surface treatment: Control (C), airborne-particle abrasion (APA), laser irradiation applying 400 mW, 600 mW, and 800 mW of 90 fs laser pulses with 1, 5, and 10 repetitions (Fs(400/1), Fs(400/5), Fs(400/10), Fs(600/1), Fs(600/5), Fs(600/10), Fs(800/1), Fs(800/5), and Fs(800/10)), respectively). Ra values were measured using a profilometer, and topographical changes were evaluated under a scanning electron microscope. X-ray diffraction analyses were performed to determine the crystallographic changes. Self-adhesive resin cement was bonded to zirconia specimens, and SBS tests were conducted. C and Fs(800/10) groups exhibited the lowest and the highest Ra and SBS values, respectively. Regardless of the fs laser power, application of five and 10 repetitions resulted in higher Ra values than air-abrasion. Fs(400/10), Fs(600/5), Fs(600/10), Fs(800/5), and Fs(800/10) groups showed higher SBS values than the APA group (p <.05), while SBS of other laser groups did not differ from the APA group (p >.05). Fs laser treatment protocols used in this study may be promising for zirconia-resin bonding. However, the effects of these treatments on the mechanical properties of zirconia need evaluation.