Hybrid nanocomposites utilize the benefits of properties of different fillers to enhance its desired properties. Polyetheretherketone (PEEK) based hybrid nanocomposites have immense potential applications in aerospace, automobile, high-temperature electrical applications, and medical and health care. The present work is an attempt to improve the elastic modulus, hardness, fracture resistance, and storage modulus simultaneously by reinforcing the PEEK matrix with multiwall carbon nanotubes (MWCNTs) filler and 30 wt.% nano hydroxyapatite (nHA)-MWCNT hybrid filler. The nanocomposites having 0,1,3,5 and 7 wt.% of MWCNTs were fabricated by the Ball Mixing and Compression Molding Method. Customized Die Heater setup was used to ensure uniform heating and cooling during compression molding. The morphology was examined by Field Emission Scanning Electron Microscopy (FESEM) and Energy-Dispersive X-ray Spectroscopy (EDS) and uniform distribution of nano-fillers was observed. The nanoindentation method was adopted to investigate the Static Mechanical Analysis (SMA) and Dynamic Mechanical Analysis (DMA) at varying frequencies of loading, of nanocomposites. At 5 wt.% of MWCNTs, the enhancements in elastic modulus, hardness, fracture resistance, and storage modulus were observed to be 80%, 36%, 32%, and 58% respectively in case of PEEK/(0–7%)MWCNT nanocomposite and 104%, 76%, 16%, and 80% respectively in case of PEEK/30%nHA-(0–7%)MWCNT hybrid nanocomposite. The decrements in loss factor indicated the improvement in elastic behavior of nanocomposites with increasing wt.% of MWCNTs. The elastic modulus of PEEK/30%nHA-5%MWCNT hybrid nanocomposite was observed to be 7.67 GPa, which falls within the range of elastic modulus of the human cortical bone. The results revealed that 5 wt.% of MWCNTs is optimum filler composition for improving the mechanical properties.