Antiretroviral therapy (ART) suppresses HIV replication, reverses immunodeficiency, and reduces AIDS-related symptoms, but non-AIDS co-morbidities like cardiovascular diseases remain a major challenge for people living with HIV (PLWH). The pathogenic mechanisms driving these co-morbidities are poorly understood. We previously showed that the HIV protein Nef contributes to chronic inflammation in PLWH. Here, we explored Nef's role in HIV-associated atherosclerosis using a novel model: HIV-infected humanized mice expressing a gain-of-function mutant of proprotein convertase subtilisin/kexin type 9 (PCSK9) and fed a high-fat diet. Comparing atherosclerosis in uninfected mice to those infected with Nef-positive or Nef-deficient HIV-1, we found that Nef exacerbates atherosclerotic changes by increasing inflammation. These results identify Nef as a key driver of HIV-related atherosclerosis and provide a platform for testing therapeutic interventions targeting Nef to mitigate cardiovascular risks in PLWH.