Sexual dimorphism is critical for the survival and propagation of many different species. In mosquitoes, sexually dimorphic behaviors include courtship, blood feeding, and oviposition site selection and are the result of both morphological differences and differences at the level of gene regulation. Gaining a better understanding of these behaviors requires an understanding of the developmental genetic basis for sexually dimorphic traits. This study utilizes a microarray-based approach to identify global gene expression profiles in male vs. female developing pupal heads of Aedes aegypti; the dengue and yellow fever vector mosquito. The dimorphism microarray revealed 2,527 significantly differentially expressed transcripts (DETs) in the pupal head. Significantly upregulated DETs in females were primarily related to proteolysis, metabolic processes, cell cycle, and cellular homeostasis gene ontology (GO) terms. The pathways that were over represented among female DETs include proteasome, glycosphingolipd biosynthesis, glycan degradation, glycosamingoglycan degradation, and glycine/serine/threonine metabolism pathways. The pathways that were over represented among male DETs include oxidative phosphorylation, alanine/aspartate/glutamate metabolism, porphyrin/chlorophyll metabolism, citrate cycle, and pyruvate metabolism. Significantly upregulated DETs in males were associated with ion transport, nucleotide metabolic/biosynthetic processes, microtubule-based processes, and cellular respiration GO terms. Whole mount in situ hybridization was used to both validate the microarray experiment and to identify regions of the brain with dimorphic gene expression. In many cases, dimorphic gene expression was localized to the optic lobe of the brain. One of the genes identified in the microarray, doublesex (dsx), was pursued further. Sex-specific expression of dsx was identified in the Ae. aegypti brain. siRNA-mediated knockdown studies demonstrated that dsx, regulates expression of a number of sex-specific DETs in the developing Ae. aegypti central nervous system. These studies identified global sex-specific gene expression profiles in the developing Ae. aegypti pupal head and identified Dsx as an important regulator of sex specific expression in the brain. This work forms a basis for understanding sexual differences in the developing Ae. aegypti CNS.