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The first nationally representative cross-sectional HIV drug resistance (HIVDR) survey was conducted in Uruguay in 2018–2019 among adults diagnosed with HIV and initiating or reinitiating antiretroviral therapy (ART). Protease, reverse transcriptase, and integrase genes of HIV-1 were sequenced. A total of 206 participants were enrolled in the survey; 63.2% were men, 85.7% were >25 years of age, and 35.6% reported previous exposure to antiretroviral (ARV) drugs. The prevalence of HIVDR to efavirenz or nevirapine was significantly higher (OR: 1.82, p < 0.001) in adults with previous ARV drug exposure (20.3%, 95% CI: 18.7–22.0%) compared to adults without previous ARV drug exposure (12.3%, 11.0–13.8%). HIVDR to any nucleoside reverse transcriptase inhibitors was 10.3% (9.4–11.2%). HIVDR to ritonavir-boosted protease inhibitors was 1.5% (1.1–2.1%); resistance to ritonavir-boosted darunavir was 0.9% (0.4–2.1%) among adults without previous ARV drug exposure and it was not observed among adults with previous ARV drug exposure. Resistance to integrase inhibitors was 12.7% (11.7–13.8%), yet HIVDR to dolutegravir, bictegravir, and cabotegravir was not observed. The high level (>10%) of HIVDR to efavirenz highlights the need to accelerate the transition to the WHO-recommended dolutegravir-based ART. Access to dolutegravir-based ART should be prioritised for people reporting previous ARV drug exposure.