Non-communicable diseases are increasing faster in HIV/AIDS patients than in the general population. We studied the association between hypertension and other possible confounding factors on viral load and CD4-cell counts in hypertensive and non-hypertensive HIV/AIDS patients receiving antiretroviral therapy (ART) at a large hospital in Eswatini over a 4-year period. We performed a retrospective longitudinal review of the medical records of 560 ART patients divided into non-hypertension and hypertension groups (n = 325 and n = 235) from July 27 to September 8, 2018. Generalized Estimated Equation was used to analyze the longitudinal data. Hypertensive patients were more likely to have improved CD4-cell counts than non-hypertensive patients (OR = 1.83, [1.37-2.44]). ART patients with hypertension were more likely to have detectable viral loads, though not significant (OR = 1.37 [0.77-2.43]). In non-hypertensive patients, second line ART was significantly associated with viral load (OR = 8.61 [2.93-25.34]) and adverse side effects (OR = 3.50 [1.06-11.54]), while isoniazid preventive therapy was significantly associated with CD4-cell counts (OR = 1.68 [1.16-2.45]). In hypertensive patients, factors associated with viral load were WHO HIV stage (OR = 2.84 [1.03-7.85]) and adherence (OR = 8.08 [1.33-49.04]). In both groups, CD4-cell counts significantly and steadily increased over time (p-value < 0.001). Results show a significant association between hypertension and CD4 cell counts but not viral load. In ART patients with and without hypertension, the factors associated with prognostic markers were different. More attention may need to be paid to ART patients with well controlled HIV status to monitoring and controlling of hypertension status.