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Background Achieving viral suppression (VS) for persons living with HIV is key to reaching epidemic control. We assessed the prevalence of VS and the frequency of HIV drug resistance mutations (HIVDRM) among children and adolescents living with HIV (CALHIV) in the Southern Highland zone of Tanzania. Methods From 2019 to 2021, we enrolled CALHIV aged 1–19 years on ART for >6 months in a cross-sectional study. Participants had viral load (VL) testing; those with VL ≥ 1000 copies/mL underwent HIVDRM testing. VS (<1000 copies/mL) prevalence estimates were calculated and robust Poisson regression was used to estimate prevalence ratios (PRs) and 95% confidence intervals (CIs) for associations with potential predictors of VS. Results Of 707 participants, 595 had VS (PR: 0.84, 95% CI: 0.81–0.87). Use of an integrase strand transfer inhibitor-containing regimen (aPR 1.15, 95% CI: 0.99–1.34), age 5–9 years (aPR 1.16, 95% CI: 1.07–1.26), and seeking care at a referral center (aPR 1.12, 95% CI: 1.04–1.21) were associated with VS. Factors inversely associated with VS included having one (aPR 0.82, 95% CI: 0.72–0.92) or two or more (aPR 0.79, 95% CI: 0.66–0.94) referrals for adherence counselling, and self-reporting missing one to two (aPR 0.88, 95% CI: 0.78–0.99) or three or more (aPR 0.77, 95% CI: 0.63–0.92) doses of ART in the past month. Of 74 participants with PRRT and INT sequencing done, 60 (81.1%) had HIVDRMs at the following frequencies: 71.6%, 67.6%, 1.4%, and 4.1% for major NNRTI, NRTI, PI, and INSTI respectively. Conclusions Higher rates of VS were observed in this cohort, and HIVDRMs were common in those without VS. This evidence supports ART optimization using dolutegravir-based regimens. However, better strategies to improve adherence are needed. [ABSTRACT FROM AUTHOR]