RP-HPLC method development was successfully done using an innovative methodology based on the design of experiments (DoE), independent component analysis (ICA), and design space (DS). The Quantification of an HIV drug combination of Emtricitabine and Tenofovir alafenamide fumarate was done using DoE. Initially, independent variables that affect the dependent variables were analyzed and the Box Behnken design was used to study the interaction between the independent variables and dependent variables. The variables selected were % of the aqueous phase, flow rate, and wavelength. These variables were then optimized using the response surface methodology. The optimization was done using 2D contour plots and 3D response surface plots which provided a defined design space that had optimized chromatographic conditions that consist of mobile phase methanol: water (40:60 v/v) with pH adjusted to 3 with orthophosphoric acid and mobile phase flow rate of 0.9 ml/min at 252 nm. The developed method was validated according to ICH Q2 R1 guidelines for system suitability parameters, linearity, accuracy, precision, sensitivity, and robustness where all the parameters were within acceptable limits. Forced degradation studies were also carried out according to ICH Q1A (R2) guidelines under acidic, basic, oxidative, photolytic, and thermal degradation. The developed RP-HPLC method was found to be precise and robust.