The effects of seven different chromatographic parameters and five sample preparation parameters in a high performance liquid chromatography (HPLC) method for assay determination of benzalkonium chloride (BKC) in a nasal formulation were evaluated using two fractional factorial experimental designs. The design space of the analytical method was modeled using Umetrics Modde software and the optimal method conditions were predicted. The optimum HPLC chromatographic conditions were obtained using a Luna CN column (150 x 4.6 mm, 3 µm). The results show that mobile phase pH, amount of acetonitrile in the mobile phase and column temperature are the most important factors in obtaining good separation of BKC homologs from an interfering peak. In the sample preparation step, the use of an aqueous solution for dissolving the samples was the most important factor since it eliminated the interfering effect of the active compound. The optimal method was validated for linearity, accuracy and precision. The use of experimental designs enables obtaining the maximum amount of information with the least possible number of experiments. Such designs are an economical manner in evaluating a variety of different factors and their interactions.