The effect of strain rate on poly(ester-ester-ketone) (PEEK) was investigated using an atomic force microscopy (AFM) based nanoindentation technique and applying a wide range of strain rates (0.012 s⁻¹–1 s⁻¹). The test results show that the average hardness and elastic modulus of PEEK follow a linear model with respect to logarithm of strain rate, from 263.9 MPa/1.377 GPa to 323.1 MPa/2.477 GPa. The maximum indentation depth decreased from 287.1 nm to 239.6 nm, indicating an enhanced densification area and shear transform zones under the indentation region. The plasticity index showed a rapid increase at low strain rate and kept stable at ∼0.640 until a strain-rate of 0.037 s⁻¹. Moreover, a ‘pile-up’ phenomenon appeared around the residual indentation area due to more free volume around the cube-corner indenter than a Berkovich indenter during the loading process.