The speed of analysis and sample throughput are very important parameters that determine the real application potential of the developed method in real practice. Various approaches are used to improve sample throughput in CE, such as multiple injection or multisegment injection strategies. However, these are only implemented in hydrodynamically open CE systems. In the present work, a simple CZE-UV method with repeated sample injection in a hydrodynamically closed separation system was developed to improve sample throughput. The nonsteroidal anti-inflammatory drug ibuprofen was selected as the model analyte. Separation was performed in a background electrolyte composed of 10 mM MOPS with 20 mM TRIS and 0.05% m-HEC. The time period between repeated sample injections was optimized, and the value of 100 s was selected as optimal. Under these conditions, it was possible to analyze three samples in one electrophoretic run. Furthermore, the developed method was characterized by excellent validation parameters. The limit of detection was predicted at the concentration level of 0.31 µg/mL and the limit of quantification at the concentration level of 1.25 µg/mL. Intra-day precision expressed as the relative standard deviation of the ibuprofen concentration ranged from 1.9 to 5.6%, and intra-day accuracy expressed as the relative error ranged from 87.1 to 106.5%. Inter-day precision was in the range of 2.6–15.0%, and inter-day accuracy was in the range of 94.9–102.7%. The developed method was then used for the determination of ibuprofen in complex pharmaceutical matrices represented by commercially available tablets and oral suspension. The determined contents of ibuprofen were in good agreement with the manufacturer´s declaration. Lastly, the developed method was evaluated according to the innovative RGB Additive Color Model strategy and was characterized by very good analytical performance parameters, safety and eco-friendliness, and practical effectiveness.