Thermal ablation (TA) has been applied in patients with low-risk papillary thyroid microcarcinoma (PTMC) who refuse surgery or active surveillance (AS). Recently, TA has been proposed as a potential therapeutic option for patients who are suitable for surgery or AS. However, the clinical outcomes of TA versus surgery remains controversial because of a lack of sufficient data. This study aimed to compare the clinical outcomes between radiofrequency ablation (RFA) versus thyroid lobectomy (TL) for low-risk PTMC in a large cohort. This retrospective study evaluated 884 patients with unifocal low-risk PTMC treated with TL or RFA from June 2014 to March 2018. Among them, 460 patients underwent TL (TL group) and 424 patients, who refused surgery or AS, underwent RFA (RFA group). Patients were regularly followed up after treatment. Local tumor progression, recurrence-free survival (RFS), complications, and treatment variables, including procedure time, estimated blood loss, hospitalization, and cost, were compared after propensity score matching (PSM). After PSM, a total of 332 patients underwent TL (mean ages 43.8 ± 9.5 years) and 332 underwent RFA (mean ages 44.1 ± 9.5 years). During the follow-up (median [interquartile ranges], 48.3 [23.2] months), no significant differences were observed in local tumor progression (1.8% vs. 3.3%,  = 0.209), lymph node metastasis (0.6% vs. 0.6%,  = 1.000), recurrent PTMC (1.2% vs. 2.4%,  = 0.244), persistent lesion (0% vs. 0.3%,  = 0.317), and 4-year RFS rates (98.2% vs. 97.0%,  = 0.223) between the TL and RFA groups. Distant metastasis was not detected. None of the patients who were treated by RFA underwent delayed surgery. Patients undergoing RFA had shorter procedure time (3.4 [2.5] vs. 86.0 [37.0] minutes,  < 0.001), lower estimated blood loss (0 vs. 20 [10.0] mL,  < 0.001), shorter hospitalization (0 vs. 7.0 [3.0] days,  < 0.001), lower cost ($2035.7 [254.0] vs. $2269.1 [943.4],  < 0.001) and lower complication rate (0% vs. 4.5%,  < 0.001) than those treated by TL. The association between treatment modality and recurrence remained nonsignificant after Cox analysis ( = 0.247). This large matched study revealed comparable four-year clinical outcomes between RFA and TL for low-risk PTMC. As a minimally invasive modality, RFA may be a promising alternative to the existing treatment options for low-risk PTMC.