The axial load capacity and stiffness of Carbon Fibre-Reinforced Polymer (CFRP) and Glass Fibre-Reinforced Polymer (GFRP) rods glued-in timber is investigated under cyclic loading as the main design consideration for structures that experience load reversal (e.g. due to wind loading). Load cycles at 20, 40, 60 and 80% of the ultimate load and three repetitions per load cycle were considered. The main parameters examined are the effect of FRP rod, anchorage length and construction scenario. The construction scenarios represent full contact between timber faces, gaps in joints due to long-term effects (e.g. viscoelastic creep) and manufacturing tolerances, and contact with other materials. The GFRP rods exhibit 23% higher axial load capacity and 20% lower axial tensile stiffness than CFRP rods for an embedment length of 5D, where D is the diameter of the rod. The axial load capacity of the GFRP rods tends to plateau with increasing bonded length at anchorage lengths greater than 10D. Small gaps significantly decrease the axial compressive stiffness of the glued-in FRP rods at the first load cycles and the axial stiffness varies along the bonded length. An analytical methodology is presented to describe the bond stress transfer mechanism and the progressive bond degradation. The analytical tensile slip values agree fairly well with the experimental results when debonding takes place at 80% of the ultimate load.