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The development of innovative therapeutic approaches that combine biocompatibility with improved anti-tumour activity is necessary, since bone cancer continues to be a major clinical problem. In this present study, hydroxyapatite (HAP) nanoparticles were synthesized using a Rutin–Arginine (Rutin-Arg) complex, which acts as a template to control crystal growth and morphology. Additionally, this complex serves as a surface functionalization agent, modifying the HAP nanoparticle surface to enhance its potential biological functionality for therapeutic applications. A template assisted wet chemical method combined with ultrasonication was used to synthesise hydroxyapatite nanoparticles with Rutin-Arg complex, improving their bioavailability, antioxidant qualities and oncotherapy potential. The synthesised nanoparticles were characterized by various analytical techniques like Fourier-Transform Infrared Spectroscopy (FT-IR), X-ray Diffraction (XRD), Field Emission Scanning Electron Microscopy (FESEM), Energy Dispersive X-ray Analysis (EDAX), High-Resolution Transmission Electron Microscopy (HRTEM), Brunauer-Emmett-Teller (BET) analysis and X-ray Photoelectron Spectroscopy (XPS). FT-IR results verified that the hydroxyapatite nanoparticles contained all functional groups. On the other hand, XRD characterisation showed distinct diffraction peaks that matched with hydroxyapatite phase, suggesting high phase purity and good crystallinity. Surface morphological analysis and elemental composition were demonstrated by FESEM with EDAX and HRTEM investigations indicated porous nanoparticles of HAP with a size range from 20 to 100 nm. A stable free radical called DPPH (2,2-diphenyl-1-picrylhydrazyl) is commonly used in the DPPH assay to evaluate a compound's antioxidant activity by detecting the colour shift from purple to yellow, which indicates a substance's capacity to neutralise free radicals. The surface functionalized HAP nanoparticles with Rutin-Arg complex exhibit a moderate level of antioxidant activity with the IC 50 value of 124.1 μg/mL. It is evident from the antioxidant capability of HAP-Rutin-Arg nanoparticles that the radical scavenging activity increased with sample concentration. The nanoparticles exhibited cytotoxic activity against MG-63 human osteosarcoma cells with an IC₅₀ value of 24.97 µg/mL, while showing biocompatibility towards normal L929 fibroblast cells. Annexin V–FITC /Propidium Iodide (PI) apoptosis assay shows that HAP–Rutin–Arg nanoparticles promote apoptosis in target cells with minimal necrosis demonstrating their potential for controlled programmed cell death. According to these in vitro results, HAP-surface functionalized with Rutin-Arginine behave as potential biocompatible nanocarrier system for osteosarcoma treatment, deserving of further study in preclinical models. • Hydroxyapatite porous nanoparticles were synthesized using a Rutin–Arginine complex as template. • The surface of HAP functionalized with Rutin-Arginine complex to enhance their biological properties. • Physiochemical characterization ensures formation of phase pure porous nano hydroxyapatite using Rutin-Arginine complex. • HAP nanoparticles functionalized with Rutin-Arginine exhibit cytotoxicity in MG-63 cells and biocompatibility with L929 cells. • Annexin V–FITC/Propidium Iodide results show HAP–Rutin–Arginine nanoparticles promote apoptosis with minimal necrosis.