Fever of unknown origin (FUO) is a common presentation for patients with advanced human immunodeficiency virus (HIV) infection and acquired immune deficiency syndrome (AIDS). We prospectively followed 72 patients, consecutively admitted to a Thai regional hospital with FUO and HIV infection to identify aetiologies and mortality in the era of available antiretroviral therapy (ART). Aetiologies of FUO were identified in 67 patients (93%), of whom 61(85%) had an infectious aetiology. The most common infectious aetiologies were Mycobacterium tuberculosis (n = 30; 42%), Cryptococcus neoformans (n = 17; 24%), Pneumocystis jiroveci (n = 9; 13%), Toxoplasma gondii (n = 5; 7%), and salmonella bacteraemia (n = 5; 7%). Nineteen patients (26%) had co-infection with two or more pathogens. The median CD4 count was 120 cells/mm3 (range, 1-581 cells/mm3), and the all-cause mortality was 22% (n = 16). By multivariate analysis, inadequate antimicrobial treatment was the sole predictor of mortality (aOR = 4.9; 95% CI = 1.2-21.9; P = 0.02). Overall, 58 of 72 patients (81%) had an opportunistic infection suggesting that guideline use of ART and prophylactic strategies remain unmet needs that will benefit individuals and populations with HIV/AIDS in Thailand.