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Rapid and efficient cell line development (CLD) process is essential to expedite therapeutic protein development. However, the performance of widely used glutamine‐based selection systems is limited by low selection efficiency, stringency, and the inability to select multiple genes. Therefore, an AND‐gate synthetic selection system is rationally designed using split intein‐mediated protein ligation of glutamine synthetase (GS) (SiMPl‐GS). Split sites of the GS are selected using a computational approach and validated with GS‐knockout Chinese hamster ovary cells for their potential to enable cell survival in a glutamine‐free medium. In CLD, SiMPl‐GS outperforms the wild‐type GS by selectively enriching high producers. Unlike wild‐type GS, SiMPl‐GS results in cell pools in which most cells produce high levels of therapeutic proteins. Harnessing orthogonal split intein pairs further enables the selection of four plasmids with a single selection, streamlining multispecific antibody‐producing CLD. Taken together, SiMPl‐GS is a simple yet effective means to expedite CLD for therapeutic protein production. [ABSTRACT FROM AUTHOR]