Abstract Background Neisseria gonorrhoeae (NG) has developed antimicrobial resistance (AMR) to multiple classes of antibiotics. While treatment of symptomatic NG in groups, such as men who have sex with men (MSM), is crucial, screening programs targeting asymptomatic NG cases may contribute to excessive antibiotic exposure of the population and thus to the emergence of gonococcal AMR. Our primary aim was to assess if intense screening could promote AMR in NG. Methods We built a network-based model of NG transmission dynamics among MSM in Belgium to estimate the prevalence of NG in the population and the risk of AMR. The model simulates daily transmission of NG among 3 anatomical sites in a population of 10 000 MSM, grouped as low risk or high risk, over 10 years. The effect of group-wise variation in treatment efficacy levels and screening intensities on NG prevalence and cumulative risk of AMR emergence was evaluated. Results Increasing screening intensity in the low-risk MSM had little effect on NG prevalence. An inverse correlation between screening intensity in the high-risk group and both NG prevalence and the risk for azithromycin resistance was observed, irrespective of the screening intensity in the low-risk group. High-risk MSM were at higher risk for azithromycin-resistant NG in all screening intensity and treatment efficacy scenarios, compared to low-risk MSM. Conclusions Our results suggest that intensive screening in the low-risk population has little impact on prevalence but may increase the probability of AMR emerging. In contrast, intensive screening in the high-risk population reduces both the prevalence of NG and macrolide resistance.