HIV/AIDS continues to be a global public health problem. Studies of the incidence and prevalence of HIV and other sexually transmitted infections (STIs) that may contribute to or aggravate its acquisition remain an effective means of prevention. In recent years, terrorist groups have established themselves in the northern regions of Cameroon. This insecurity has led to a large influx of refugees with no information about their HIV and STI status. Given this above mentioned situation, this study aimed to assess the incidence and prevalence of HIV and STI and their associated risk factors in order to adjust strategies to monitor the epidemic. A cohort of 684 consenting participants from the North and Far North were enrolled in the study in 2021 and followed up in 2022 to measure the incidence and prevalence of HIV and to assess some associated risk factors. Each participant was administered a pretested questionnaire to collect sociodemographic variables and risk behaviors. Anti-HIV Ab, HBsAg (Hepatitis B Surface Antigen), TPHA (Treponema Pallidum Hemagglutination Assay) tests were performed. The data were compiled using EPI Info 7.5.2 for epidemiological analyses. The association between co-infections of HIV, Hepatitis, and syphilis and HIV incidence was evaluated using the Chi-2 test. The HIV incidence and overall prevalence were 1.63% (163/10,000 population) and 3.8%, respectively. The HIV incidence increased from 0.27% in 2017 (DHS) to 1.63% in the North and Far North regions as found in our study. The incidences of syphilis and hepatitis B were 1.03% and 4.56%, respectively. Factors associated with HIV acquisition included religion (Muslims being more infected, P<0.03), unprotected sex with a new partner (P<0.007), having a sex worker as a partner (P<0.0001), and co-infection with syphilis and hepatitis B (P<0.05). The findings also link increased HIV incidence to insecurity and population displacement. In HIV prevention strategies, it is important to consider the security and political stability context as well as HIV-associated infections such as hepatitis B and syphilis.