A new analytical quality by design-assisted HPLC–UV approach is presented, for the first time, for the concurrent determination of cetirizine (CTZ) and azelastine (AZE) in raw materials, commercial eye drops and aqueous humor. The two drugs are co-administered as eye drops in severe ocular allergies. A 23 full factorial design was adopted for the chromatographic optimization to ensure the best analytical performance and reliability, as well as to save time, effort and solvent consumption. The parameters, including pH, acetonitrile ratio, and flow rate, were selected as independent factors. The responses analyzed were resolution and tailing of peaks. The separation was achieved through isocratic elution on C8 column with mobile phase made up of acetonitrile: 0.3% triethylamine of pH 5 (60:40 v/v) at a flow rate of 1.2 mL min−1 and detection at 216 nm. The elution time was less than 6 min. The approach was fully validated in accordance with International Council for Harmonization (ICH) guidelines. Good linearity was achieved over the concentration ranges of 1.0–30 and 0.5–10 µg mL−1 with limits of detection of 0.310 and 0.158 µg mL−1 and limits of quantification of 0.940 and 0.479 µg mL−1 for CTZ and AZE, respectively, with correlation coefficients of 0.9998. The intra- and inter-day precisions were lower than 2%. The good sensitivity of the approach permits the analysis of CTZ and AZE in spiked aqueous humor with mean percentage recoveries of 100.93 ± 1.42 and 100.11 ± 1.55, respectively. The statistical comparison between results of the developed method and the comparison method revealed no differences, indicating the accuracy of the method.