Aedes is an important vector for various viruses that cause dengue, chikungunya and zika, which affect human health globally. Due to regular outbreaks of these diseases worldwide, there is a need to identify essential vector proteins that are critical for the survival of the vector, which may be targeted to control the spread of vector-borne disease (VBD). In silico computational methods involving comparative proteomics, analysis of orthologous proteins common amongst members of Aedes genus and protein-protein interaction (PPI) pathway were used to identify essential proteins that could act as novel therapeutic candidates. Twenty-three conserved proteins between A. aegypti and A. albopictus were identified from a BLASTP search with an e-value threshold of 0.005, and their PPI networks were constructed in the STRING database. The merged network was analyzed using various Cytoscape plugins viz. ClusterONE, Cytohubba and MCODE. Thirty-one hub proteins were identified from the system's network biology analysis, and detailed data and literature mining were carried out. Twelve novel vector-control target proteins of A. aegypti, having no human homologs, were determined in the present study that can effectively act as potential therapeutic candidates for drug design and vaccine development.