The use of plant extracts provides a biologically inspired route for the synthesis of nanoparticles, which have received a significant interest worldwide. ZnO nanomaterials have been one of the most comprehensively researched materials for decades and still hold attention of researchers in the field of biosensing. In the present study, a systematic approach was used for the green synthesis of zinc oxide nanoparticles (ZnO NPs) with an average size of 4-8 nm using Carica papaya seed extract. The prepared ZnO NPs were characterized using X-ray diffraction (XRD), Transmission electron microscopy (TEM), UV-visible spectroscopy and Fourier transform infrared spectroscopy (FTIR). The composition of the extract was identified using gas chromatography mass spectrometry (GCMS), which revealed the role of oleic acid as an important capping agent in the synthesis of ZnO NPs. To investigate the electrochemical application, the synthesized ZnO NPs were further tested for sensing activities of silymarin by integrating them with multiwalled carbon nanotubes (MWCNTs) on the glassy carbon electrode (GCE). The electrochemical signals obtained from MWCNTs/ZnO NPs/GCE were 2-fold higher than MWCNTs/GCE and bare GCE. Electrochemical detection using our applied protocol with the developed MWCNTs/ZnO NPs composite could detect 122 mg of silymarin in the 160 mg quoted concentration, in the commercial Milk Thistle tablet, confirming an efficiency of detection that is approximately 76%. The present study has highlighted the environmentally benign and cost effective route for the synthesis of ZnO NPs using Carica papaya seed extract. These NPs were found to possess enhanced sensing applications. To understand the electrochemical sensing of silymarin by ZnO NPs at the molecular level, the interaction of silymarin with ZnO model clusters, (ZnO) with n = 3 and 4 was investigated using density functional theory (DFT) using B3LYP functional and 6-311 + G/LanL2DZ basis set. The charge transfer from ZnO clusters to -OH group of silymarin which strengthens the interactions between silymarin molecule and ZnO clusters were analyzed in terms of interaction energies and stabilization energies derived by second order perturbation energies. The obtained energies indicated the most probable position and functional groups in silymarin, which led to its binding with ZnO NPs and detection. The strategy for the electrochemical detection of silymarin applied in present work serves as a systematic benchmark to assess the electrochemical biosensing of potential biomolecules in the presence of different metal oxide NPs.