The control of mosquito breeding is an essential step towards the reduction of vector-borne disease outbreaks. Synthetic larvicidal agents produce resistance in vectors and cause safety concerns in humans, animals and aquatic species. The drawback of synthetic larvicides opened a new avenue for natural larvicidal agents, but poor dosage accuracy, need for frequent applications, low stability and sustainability are the major challenges with them. Hence, this investigation aimed to overcome those drawbacks by developing bilayer tablets loaded with neem oil to prevent mosquito breeding in stagnant water. The optimised batch of neem oil-bilayer tablets (ONBT) had 65%w/w hydroxypropyl methylcellulose K100M and 80%w/w ethylcellulose in its composition. After the completion of 4th week, 91.98 ± 0.871% azadirachtin was released from the ONBT, which was followed by a subsequent drop in the in vitro release. ONBT reported long-term larvicidal efficacy (>75%) and a good deterrent effect which was better than neem oil-based marketed products. The acute toxicity study on a non-target fish model (Poecilia reticulata), OECD Test No.203 confirmed the safety of the ONBT on non-target aquatic species. The accelerated stability studies predicted a good stability profile for the ONBT. The neem oil-based bilayer tablets can be used as an effective tool for the control of vector-borne diseases in society. The product may be a safe, effective and eco-friendly replacement for the existing synthetic as well as natural products in the market.