Syphilis, a sexually transmitted infection, has reemerged in many vulnerable groups around the world. The objective of the current study was to determine the prevalence and incidence of syphilis among people who attended a specialized HIV clinic in Mexico from 2011 to 2015. Databases from the laboratory were analyzed, and the following four groups were formed: people seeking HIV-1 voluntary counseling and testing (VCT), people in prison (PPr), people living with HIV (PLWH), and patients from primary care clinics (others). The diagnosis of syphilis was made using the reverse algorithm; antibody titers were examined to determine the stage of infection. Baseline data were analyzed and, with follow-up information, a retrospective dynamic cohort was formed. Factors associated with the seroprevalence of syphilis and active syphilis were evaluated by the chi-square test. Moreover, risk factors for the incidence of syphilis were described. A total of 81,863 baseline individuals were analyzed. The seroprevalence of syphilis was 9.9% in the VCT group, 8.2% in the PPr group, 37.0% in the PLWH group, and 8.7% in the others group; the prevalence of active syphilis was 1.7–13.1%. A total of 11,124 people were followed up. The incidence (cases per 100 person-years) was 3.5 among the VCT group, 16.0 among the PLWH group, and < 0.1 among both the PPr and others groups, respectively; moreover, the frequency of reinfections was 11.1–24.4%. The high prevalence and incidence of syphilis, active syphilis, and reinfections among men, transgender people, individuals aged 20–39 years, and people with a history of HIV or hepatitis B suggest that it is critical to improve prevention, diagnosis, and treatment measures to stop the reemergence of syphilis. There are also new factors such as methamphetamine use, group sex, or contacting partners over the internet that are associated with syphilis. In addition, HIV preexposure prophylaxis could contribute to the increased incidence of syphilis by providing false security in the prevention of STIs, thereby increasing risky sexual behaviors.