In this paper, we describe a facile method for preparation of ZnSe quantum dots (QDs) using an inexpensive and biocompatible source of acetyl cysteine in aqueous media. The structural properties of the ZnSe QDs have been characterized using XRD, FT-IR, and TEM techniques. The optical properties of the as-prepared QDs were found to be size-dependent, due to the strong confinement regime at relatively low refluxing time. Effect of solution pH and refluxing temperature on absorption and emission characteristics of the ZnSe QDs was studied. The empirical effective mass approximation also reveals that, both solution pH and refluxing temperature parameters would effect on ZnSe QDs growth, and increase their size. However, the influence of the solution pH was found to be more prominent.Water-solubility, high emission intensity and sub-10 nm nanocrystals size are the most essential features that suggest our synthesized aqueous-based ZnSe QDs (with a very cost-effective and biocompatible capping agent) can be utilized for biological intentions.