Despite the excellent osseointegration of carbon-fiber-reinforced polyetheretherketone (CFR/PEEK) with a surface hydroxyapatite (HA) coating, the bone-implant interfacial shear strength of HA-coated CFR/PEEK after osseointegration is unclear. We examined the interfacial shear strength of HA-coated CFR/PEEK implants after in vivo implantation in a rabbit femur-implant pull-out test model. HA coating was performed by a newly developed method. Uncoated CFR/PEEK, HA-coated blasted titanium alloy, and uncoated blasted titanium alloy were used as control implants. The implants were inserted into drilled femoral cortex, and pull-out tests were conducted after 6 and 12 weeks of implantation to determine maximum interfacial shear strength. The HA-coated CFR/PEEK (15.7 ± 4.5 MPa) and HA-coated titanium alloy (14.1 ± 6.0 MPa) exhibited significantly larger interfacial shear strengths than the uncoated CFR/PEEK (7.7 ± 1.8 MPa) and the uncoated titanium alloy (7.8 ± 2.1 MPa) at 6 weeks. At 12 weeks, only the uncoated CFR/PEEK (8.3 ± 3.0 MPa) exhibited a significantly smaller interfacial shear strength, as compared to the HA-coated CFR/PEEK (17.4 ± 3.6 MPa), HA-coated titanium alloy (14.2 ± 4.8 MPa), and uncoated titanium alloy (15.0 ± 2.6 MPa). Surface analysis of the removed implants revealed detachment of the HA layer in both the HA-coated CFR/PEEK and titanium alloy implants. The proposed novel HA coating method of CFR/PEEK significantly increased interfacial shear strength between bone and CFR/PEEK. The achieved interfacial shear strength of the HA-coated CFR/PEEK implant is of the same level as that of grit-blasted titanium alloy with HA.