Background The “test-and-treat” policy may adversely affect adherence to clinic visits of clients newly diagnosed with HIV due to unpreparedness to commence treatment. However, few studies have examined the factors influencing the status of adherence to second clinic visit among clients newly diagnosed with HIV. We examined the factors influencing the status of adherence to second clinic visit among clients newly diagnosed with HIV in Apac District, northern Uganda. Methods This was a mixed-methods study conducted among 292 systematically sampled clients newly diagnosed with HIV for the survey and 15 purposively sampled clients for the in-depth interview from July to August 2020. Quantitative data were collected using a structured questionnaire, while qualitative data were collected using an interview guide. Quantitative data were analyzed descriptively while qualitative data were analyzed thematically. Results The mean age of the study participants were 39.5±11 years and their age ranged from 18 to 72 years. Close to three-quarters of study participants adhered to their second clinic visit 74% (214/292). Factors that influenced participants’ adherence to the second clinic visit were the adequate HIV pre/post-test counseling positive attitude of clients towards HIV-positive diagnosis, family support, and long waiting time. Conclusion More than two-thirds of clients newly diagnosed with HIV in Apac District, northern Uganda adhered to their second clinic visit. HIV/AIDS service providers should strengthen HIV pre/post-test counselling, social support systems for persons living with HIV/AIDS, and reduce clients’ waiting time to improve adherence to second clinic visit among clients newly diagnosed with HIV.