OBJECTIVE: To compare the clinical outcomes of patients with unifocal paratracheal papillary thyroid microcarcinoma (PTMC) after thermal ablation (TA) vs. partial thyroidectomy (PT). MATERIALS AND METHODS: This retrospective multicenter study included 436 patients with unifocal, clinical N0 paratracheal PTMC who underwent TA (210 patients) or PT (236 patients) between June 2014 and December 2020. The propensity score matching method was used to mitigate confounding factors between the two groups. Disease progression, progression-free survival (PFS), complications, and treatment variables were compared. Adjusted Cox regression models were utilized to assess the impact of treatment on disease progression. RESULTS: After matching, a comparable incidence of disease progression (3.3% vs. 2.2%, p = 0.79) and comparable 5-year PFS rates (97.0% vs. 97.4%, p = 0.75) were observed between the TA and PT groups. Adjusted Cox regression models showed no significant correlation between TA and disease progression. TA was associated with shorter hospitalization (0 vs. 6.0 days), less estimated blood loss (0 vs. 15.0 mL), shorter incision length (0.3 vs. 6.0 cm), and lower costs ($1748.3 vs. $2898.0) compared with PT (all p < 0.001). The complication rate was 1.1% after TA and 3.3% after PT (p = 0.28), with permanent complications were exclusively observed in the PT group. CONCLUSION: The mid-term incidence of disease progression and PFS rates were similar between TA and PT in patients with unifocal paratracheal PTMC. TA might represent a promising alternative treatment to PT for eligible patients with paratracheal PTMC. KEY POINTS: Question Is thermal ablation a viable alternative treatment to partial thyroidectomy for treating paratracheal papillary thyroid microcarcinoma? Findings Comparable incidence of disease progression and 5-year progression-free survival rates were observed between thermal ablation and partial thyroidectomy. Clinical relevance Thermal ablation, as a minimally invasive procedure, provides a promising alternative to partial thyroidectomy, with comparable clinical outcomes for patients with paratracheal papillary thyroid microcarcinoma.