The bioavailability of drugs can be improved by regulating the structural properties, particularly lipoid systems, such as niosomes, can increase cellular uptake. Herein, we optimized double emulsion and niosomal formulations for encapsulating anthocyanin-rich black carrot extract. Nanoparticles obtained by selected formulation were characterized in terms of morphology, particle size, drug encapsulation efficiency, in vitro release and cytotoxicity. The optimum conditions for niosomal formulation were elicited as 30 mg of cholesterol, 150 mg of Tween 20 and feeding time of 1 min at a stirring rate of 900 rpm yielding the lowest average particle size of 130 nm. In vitro release data showed the majority of the encapsulated anthocyanins were released at the end of 10 h. A mathematical model was developed to estimate the absorption of anthocyanins released from niosomes and cytotoxicity was assessed against neuroblastoma. Overall, these findings suggest that niosomal vesicles might be suitable delivery systems for anthocyanins.