Harvesting microalgae from water and wastewater streams is important for both environmental remediation and re-cycling of both algal material and associated nutrients. Chitosan is widely used as an environmentally friendly flocculant in this process. Charge neutralization is a key operating mechanism for chitosan flocculation in microalgae harvesting. Alkaline conditions have been conventionally used to modify chitosan to create an increase in charge neutralization. However, it is often difficult to operate the chemical processes needed for this method, which also pose environmental risks. In this study, a simple and environmentally safe method to increase chitosan charge neutralization using electrolysis was proposed and tested in the harvest of microalgae. The results demonstrate that the electrolysis produced a charging effect on the chitosan and exhibited a significant positive relationship with current intensity (r2 = 0.91, P < 0.05). When the electrolysis was operated at 0.2, 0.4, and 0.6 A, the charge neutralization of chitosan increased by 2.05, 4.99, and 10.86 mV/mg, respectively. As the charge neutralization increased, chitosan flocculation yielded a higher microalgae harvesting efficiency at a lower chitosan dosage. One of the possible mechanisms for the increased charge neutralization ability is the deacetylation of the acetyl groups caused by electrolysis. This idea needs further study that includes identifying a chitosan structure change. This study proposed a novel strategy for modifying chitosan and its derivatives for enhancing flocculation in microalgae-based engineering.