Gonorrhea, caused byNeisseria gonorrhoeae(N. gonorrhoeae), is a persistent global public health threat. The development of low-cost, point-of-care testing is crucial for gonorrhea control, especially in regions with limited medical facilities. In this study, we integrated CRISPR/Cas12a reaction with recombinase polymerase amplification (RPA) to provide a simple and adaptable molecular detection method forN. gonorrhoeae. The RPA-Cas12a-based detection system developed in this study enables rapid detection ofN. gonorrhoeaewithin 1 h without the use of specialized equipment. This method is highly specific for identifyingN. gonorrhoeaewithout cross-reactivity with other prevalent pathogens. Furthermore, in the evaluation of 24 clinical samples, the detection system demonstrates a 100% concordance rate with traditional culture, which is being used clinically as a reference method. Overall, the RPA-Cas12a-basedN. gonorrhoeaedetection has the advantages of rapidity, portability, low-cost, no special equipment required, and strong operability, and has a high potential for application as a self-testing and point-of-care diagnosis, which is critical for the clinical management of gonorrhea in developing countries lacking medical equipment.Graphical AbstractSupplementary InformationThe online version contains supplementary material available at 10.1186/s13568-023-01554-7.