HIV disproportionately affects men who have sex with men (MSM) and transgender women (TW). These populations use alcohol more heavily than the general population, and alcohol use disorders (AUDs) are more prevalent among them. Naltrexone (NTX) has documented efficacy and safety as a medication-assisted therapy for AUD. Its use has not been well-examined in persons with HIV (PWH) newly initiating antiretroviral therapy (ART) where the possibility of hepatotoxicity may be increased when initating multiple new medications. This study assessed the safety of oral NTX treatment (50 mg daily) initiated concomitantly with antiretroviral therapy (ART) in a double-blind randomized placebo-controlled trial of NTX in MSM/TW in Lima, Peru among MSM and TW with AUD (AUDIT score ≥ 8). We analyzed adverse event data from ART-naïve participants (N = 155) who were randomized (2:1) to initiate ART plus NTX (N = 103) or ART plus placebo (N = 52). Participants were monitored for 24 weeks while taking ART plus NTX/placebo, followed by 24 weeks receiving ART alone. Over 48 weeks, 135 grade 2 or 3 adverse events were reported, resulting in 1.3 clinical adverse events per participant equally represented in both treatment and placebo arms. Two serious adverse events occurred among two participants receiving NTX; neither was attributed to the study medication. No significant differences were found in the proportion of subjects reporting any adverse events between treatment arms across all time-points. These results suggest NTX is safe in MSM/TW PWH with AUD newly initiating ART, as no excess of clinical adverse events or transaminase elevation was associated with NTX use.