Deep eutectic solvent (DES) combined with ultrasonic-assisted extraction was employed as an environmentally friendly technique for extracting antioxidant phenolic compounds from Neem leaves in place of organic solvents. Choline chloride-Ethylene glycol (1:2) with 40% V/V water content (DES-1) was investigated as a potential total phenolic content extractant (38.2 ± 1.2 mg GAE/g DW, where GAE: gallic acid equivalent, DW: dry weight). The optimal operational parameters assessed using single-factor experiments to maximize the total phenolic compounds content were as follows: extraction time of 30 min, 40% V/V water content, liquid-solid ratio of 15:1, and room temperature. Additionally, the in-vitro antioxidant experiments (2,2-diphenyl-1- picrylhydrazyl radical scavenging assay and ferric reducing antioxidant power assay) demonstrated the DES-1-based extract of Neem leaves as a potent antioxidant agent, compared to traditional solvents. Moreover, microscopic morphological analysis supported the effectiveness of DES-1 for the noticeable alteration in the fiber surface structure of Neem leaves after extraction which benefited in the release of polyphenols from these leaves. Eventually, the mass analysis of the extract disclosed the presence of eleven polyphenols in the extract. The Green Analytical Procedure Index revealed the greenness of the extraction method.