Culex pipiens is a mosquito responsible for the transmission of various vector-borne diseases including elephantiasis and West Nile Fever (WNF) to the humans. The aim of the current work is to find a mosquito control method that is effective, safe and affordable that can be used in a variety of communities where these disease vectors are a problem. This study is carried out by evaluating the larvicidial, biochemical and histological effect of various concentrations of Balanites aegyptiaca extracts on the Culex pipiens third instar larvae. The median lethal concentration )LC50 (was determined and then used to make a histological and biochemical studies with LC50 value for leaves 21.5 %, for fruits 63.26 %. An aqueous extract of Balanites aegyptiaca leaves and fruits was tested serious of different concentrations between 10 and 100% were prepared and applied to the larvae. The tested Balanites aegyptiaca induced many changes on the third instar treated larvae as follows, the activity levels increase in the alpha amylase case, the total protien and the acid phosphatase levels decrease, lactate dehydrogenase and alkaline phosphatase activity levels were disturbed. Histological studies revealed that the treated larvae had undergone obvious changes in muscles, cuticle and midgut. Overall, this research indicates that using Balanites aegyptiaca fruits and leafs extract may be useful for controlling Cx. pipiens.