Plant-based medicines have been a part of primary healthcare since time immemorial. Natural products have received increasing attention to treat several regenerative diseases due to their availability and fewer side effects than conventional drugs. Towards this, Neem, commonly known as ‘Divine Life-giving tree’, has been investigated for its efficiency against MCF7, breast cancer cell lines. Ethanolic neem extracts were analysed for qualitative phytochemical screening tests, spectral analysis, antioxidant activity, and total phenol contents. In addition, to enhance the recovery of secondary metabolites from the plant extracts, electroporation (EP) technique is used. The effect of EP was studied by comparing with untreated extracts, which exhibits antioxidant activity (∼96% increase) and total phenol contents (∼12.51% increase) than untreated extracts. This indicates that electroporated extract (EE) exhibited higher antioxidant and phenolic activity than other extracts. Furthermore, different concentrations of untreated and electroporated neem extracts were used to study the anti-cancer activity. To enhance the uptake of extracts against cell membranes, electrical pulses of EP1 = 1200 V/cm, 100 s, 8 pulses and, EP2 = 500 V/cm, 20 ms, 8 pulses were used. The results indicate cell viabilities of 35% with untreated extract only, 5.6% with EE, 3.17%, and 2.49% with EP1 + EE extract and EP2 + EE extract, respectively, indicating the potential of the synergy of electrical pulses + EE. The viabilities were lowered by 5–6 times after 72 h. This treatment is more appropriate to achieve maximum cell death, thereby reducing the side effects of conventional drugs in treating breast cancer.