Sterol carrier protein-2 (SCP-2) is a non-specific intracellular lipid carrier protein. However, the molecular mechanism of ligand selectivity and the in vivo function of SCP-2 remain unclear. In this study, we used site directed mutagenesis to investigate ligand selectivity and in vivo function of the yellow fever mosquito sterol carrier protein-2 protein (AeSCP-2). Mutations to amino acids in AeSCP-2 known to interact with bound ligand also decreased NBD-cholesterol binding. Substitution of amino acids in the ligand cavity changed the ligand specificity of mutant AeSCP-2. Over-expressing AeSCP-2 wild-type in the Aedes aegypti cultured Aag-2 cells resulted in an increase in incorporation of [3H]cholesterol. However, over-expressing mutants that were deleterious to the binding of NBD-cholesterol in AeSCP-2 showed a loss in the ability to enhance uptake of [3H] cholesterol in cultured cells. Interestingly, when [3H]palmitic acid was used as the substrate for incorporation in vivo, there was no change in the levels of incorporation with over-expression of wild-type protein or mutated AeSCP-2s. The in vivo data suggest that AeSCP-2 is involved in sterol uptake, but not fatty acid uptake. This is the first report that the ability of cholesterol binding may directly correlate to AeSCP-2’s in vivo function in aiding the uptake of cholesterol.