The aim of the study was to evaluate the human immunodeficiency virus (HIV) treatment cascade and mortality in migrants and citizens living with HIV in Botswana. Retrospective 2002 to 2016 cohort study using electronic medical records from a single center managing a high migrant case load. Records for 768 migrants and 3274 citizens living with HIV were included. Maipelo Trust, a nongovernmental organization, funded care for most migrants (70%); most citizens (85%) had personal health insurance. Seventy percent of migrants and 93% of citizens had received antiretroviral therapy (ART). At study end, 44% and 27% of migrants and citizens, respectively were retained in care at the clinic ( P < .001). Among the 35% and 60% of migrants and citizens on ART respectively with viral load (VL) results in 2016, viral suppression was lower among migrants (82%) than citizens (95%) ( P < .001). Citizens on ART had a median 157-unit [95% confidence interval (CI) 122–192] greater increase in CD4+ T-cell count (last minus first recorded count) than migrants after adjusting for baseline count ( P < .001). Five-year survival was 92% (95% CI = 87.6–94.8) for migrants and 96% (95% CI = 95.4–97.2) for citizens. Migrants had higher mortality than citizens after entry into care (hazard ratio = 2.3, 95% CI = 1.34–3.89, P = .002) and ART initiation (hazard ratio = 2.2, 95% CI = 1.24–3.78, P = .01). Fewer migrants than citizens living with HIV in Botswana were on ART, accessed VL monitoring, achieved viral suppression, and survived. The HIV treatment cascade appears suboptimal for migrants, undermining local 90-90-90 targets. These results highlight the need to include migrants in mainstream-funded HIV treatment programs, as microepidemics can slow HIV epidemic control.