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We aimed to assess the temporal trends of incident syphilis and its associated risk factors among men with HIV (Human Immunodeficiency Virus) in Korea during the COVID-19 pandemic. We conducted a retrospective cohort study of men with HIV attending an HIV clinic in Korea between 2005 and 2022. Of 767 men with HIV, 499 were included and contributed 3220 person-years (PY) of the observation period. Eighty-two patients were diagnosed with incident syphilis, with an overall incidence of 2.55/100 PY (95% confidence interval [CI] 20.56–31.53). The incidence of syphilis per 100 PY gradually decreased from 2.43 (0.79–7.42) in 2005–2007 to 1.85 (1.08–3.17) in 2014–2016; however, it increased to 3.0 (1.99–4.53) in 2017–2019, and further to 3.33 (2.26–4.89) in 2020–2022. A multivariate analysis identified young age (≤30 years versus >50, adjusted HR 6.27, 95% CI 2.38–16.56, p < 0.001), treponemal test positive at baseline (2.33, 1.48–3.67, p < 0.001), men who have sex with men (2.36, 1.34–4.16, p = 0.003), and history of incarceration (2.62, 1.21–5.67, p = 0.015) as risk factors for incident syphilis. Recently, syphilis incidence in men with HIV has increased in Korea, especially in young patients and at-risk groups, highlighting the need for enhanced regular screening and targeted behavioral interventions among these populations.