This study was designed to evaluate the shear bond strength of an adhesive/composite system subjected to different pretreated polyetheretherketone (PEEK) surfaces using different thermocycling conditioning methods. A total of 128 specimens were equally divided into four main groups (n = 32/group): control (no pretreatment), air abrasion, argon plasma pretreatment, and femtosecond laser groups. The surface topographies and surface roughness were observed by atomic force microscopy after different pretreatments. The specimens were bonded with SE Bond/Clearfil AP-X™. All bonded specimens were stored in distilled water at 37°C for 24 h. Afterward, each group was divided into three subgroups (n = 8/group) as follows: (a) stored in water for 56 h (37°C); (b) thermal aging for 5000 cycles (5°C/55°C); and (c) thermal aging for 10,000 cycles (5°C/55°C). The shear bond strengths were measured. Air abrasion, argon plasma pretreatment, and femtosecond laser significantly strengthened the bond of SE Bond/Clearfil AP-X™ to PEEK composite compared with that without additional pretreatment. In the same surface pretreatment, the shear bond strengths of specimens conditioned using water storage were higher than that using thermocycles (TCs). Additionally, the specimens with 5000 TC showed significantly higher shear bond strength than that with 10000 TC.