Introduction Thyroid dysfunction is one of the most common endocrine disorders in people living with HIV (PLHIV). The abnormality in thyroid function has been linked with the adverse effects of prolonged antiretroviral therapy (ART) in PLHIV, but its prevalence remains obscure. The present study aimed to determine the prevalence of impaired thyroid function and its relationship to ART duration in Nepalese people living with HIV. Methods This cross-sectional clinical laboratory based study was conducted at SRL Diagnostics Nepal, Pvt. Ltd. from October 2021 to May 2022. Two hundred and three HIV-seropositive patients enrolled at Tribhuvan University Teaching Hospital (TUTH) in Kathmandu, Nepal were examined for their thyroid function test (TFT) by analyzing the serum T3, T4, and TSH concentrations using a fully automated COBAS e411 analyzer (Roche Diagnostics, USA) based on the electrochemiluminescence assay (ECLIA). Results Out of 203 PLHIV, 22 (10.83%) had a thyroid disorder, with subclinical hypothyroidism ( n = 16, 72.73%) being the most common, followed by subclinical hyperthyroidism ( n = 3, 13.63%). Thyroid dysfunction had no significant correlation with HIV/ART duration ( p = 0.304) and sex ( p = 0.419), whereas, the risk of thyroid dysfunction was induced with the rise in the age of the PLHIV ( p = 0.002, ϕ = 0.274). There were no significant differences in the mean serum T3, T4 and TSH values among different sexes and the HIV/ART duration, however a significant difference in the mean values of TSH (F (3, 199) = 3.231, p = 0.023) and T3 (F (3, 199) = 4.587, p = 0.004) among the different age-groups were shown. The mean T3 values also indicated a gradual decrease with increasing age. Conclusion The study revealed subclinical hypothyroidism as the prevailing thyroid disorder associated with PLHIV. The risk of thyroid dysfunction in PLHIV was neither gender specific nor being attributed by the ART duration in Nepalese population; however, elderly PLHIV were highly susceptible to the risk of thyroid disorder.