The present study includes the Azadirachta indica (neem) induced Silver nanoparticles (AgNPs) by green synthesis as reducing and capping agent. Synthesized AgNPs were characterized by different instrumental techniques such as XRD (X-ray Diffraction), SEM (Scanning Electron Microscopy), TEM (Transmission Electron Microscopy), Zetasizer, UV-Visible and FT-IR (Fourier Transformation Infra-Red) spectroscopy. The result of XRD reveals that nanoparticles were crystalline in nature and pure, stability was determined by Zeta potential and SEM, TEM analysis indicates that AgNPs was monodisperse in a spherical shape with average size 9 nm. These synthesized AgNPs were applied as the catalyst in the degradation process of Methyl Orange (MO) and wastewater samples in presence of peroxodisulphate (PDS). Effect of different experimental conditions such as initial pH, concentration of PDS, Dye, and AgNPs was studied on the degradation process. The obtained kinetic result shows that AgNPs/PDS system induces 1.1 × 10−4 to 15.9 × 10−4 s-1 folds in presence of the small concentration of AgNPs (1 × 10−8 mol dm−3). The degradation of MO and real wastewater samples in AgNPs/PDS system is followed pseudo-first order kinetics and maximum degradation of MO reached 88% in 40 min and real wastewater samples in 80 min. Liquid chromatography-mass spectrometry (LC-MS) analysis and UV-Visible spectral changes were used to analyze the structure of intermediate and end products (CO2, H2O, NO3−, and O3S−) during the degradation process. Furthermore, the result of biodegradability index (greater than 0.3) implies that advanced oxidation process enhances the biodegradability of wastewater.