Progression of health in HIV patients on ART is characterized by an increase in CD4 cell counts as well as a decrease in viral load (HIV RNA) to undetectable levels. Monitoring and evaluation of HIV occurrence and responses allow countries to track the epidemic and its prevention and control efforts. This study assessed the use of viral load and CD4 cell counts in monitoring HIV progression. Various plausible transition autoregressive models, to account for the dependence in CD4 counts and viral load, were fitted using R software version 4.4.1. The transition autoregressive mixed model of order three, AR(3), and of order four, AR(4), proved helpful in analyzing viral load and CD4 cell count data, respectively. There was higher and significant between-patient variation than between-hospital variation in both viral load and CD4 cell counts. Thus, understanding individual patient-based unmeasured factors is crucial in determining viral load and CD4 cell count outcomes than hospital-based variables.