Transoral Robotic Surgery (TORS) has become widely adopted for the surgical removal of oropharyngeal squamous cell carcinoma (OPSCC), with the most common locations being in the tonsil and base of tongue (BOT). However, it is currently unknown if TORS has equal efficacy and outcomes in patients with tonsillar or BOT OPSCC. Therefore, the aim of this study was to compare the margin status and recurrence rates of tonsillar and BOT OPSCC after TORS. Per PRISMA guidelines, PubMed, Scopus, and CINAHL were systematically searched from inception to 2/28/2022. Articles including the surgical management of OPSCC with TORS that compared margin status, complications, and recurrence between tonsil and BOT were included. Meta-analyses of proportions and odds ratios were performed. A total of 28 studies were included, comprising 1769 patients with tonsillar OPSCC and 1139 patients with BOT OPSCC. HPV positivity was seen in 92.3% of tumors. BOT OPSCC had a higher rate of positive margins compared to tonsillar OPSCC (28.1% [95%CI 15.1–43.3] vs. 7.5% [95%CI 3.3–13.3]). No differences were seen in recurrence between BOT and tonsillar OPSCC (OR 1.1 [95%CI 0.8–1.5], p = 0.480). In addition, no differences in postoperative hemorrhage were seen between tonsillar and BOT OPSCC (10.7% [95%CI 6.1–16.5] vs. 8.8% [95% CI 1.5–21.3]). While a higher rate of positive margins was seen in BOT OPSCC when compared to tonsil OPSCC, this did not translate to a higher recurrence rate in the BOT group. Future research on which subset of patients with BOT is more likely to have positive margins is warranted to improve the utility of TORS further.