Background: The progression of human immunodeficiency virus (HIV) infection to acquired immunodeficiency syndrome (AIDS) and eventually to death can be considered a stochastic process, which can be broken down into a finite number of intermediate states, based on CD4 counts. To assess ART in terms of effectiveness and to help guide public health decisions-making, it is critical to account for both the short- and long-term effect of ART in HIV progression. This chapter models the progression of HIV/AIDS disease in patients receiving ART in Namibia using homogeneous semi-Markov processes. Methods: A retrospective study design was used to obtain data on 2422 patients who were observed 11,028 times. The homogeneous semi-Markov model was employed to estimate the transition probabilities and transition intensity rate and assess effectiveness of ART by comparing the forward transition and reverse transitions. Results: It was shown that the probabilities of transiting from state 1 to 3 and 4 were 0.023 and 0.004 after 6 months and 0.059 and 0.010 after 12 months, respectively. As expected, the intensity indicates that the rate of transiting from good states to worst states is decreasing. The strongest predictor of transition from state 1 to 2 is Efavirenz/lamivudine/tenofovir (TDF/3TC/EFV), which has a hazard ratio of 1.338 (with p value of 0.002). A hazard ratio of 0.678 for the predictor variable female shows that female were less likely to transit from state 2 to 3 than their male counterparts. The hazard ratios of females from a bad state to a better state are more than 1, which is an indication that females are less likely to respond to treatment compared to males. Conclusion: HIV can progress to AIDS without delay if there is no intervention. Early ART initiation is crucial to reduce the probabilities of transiting from good states to worse states.