Thyroidectomy is a common operation, performed by general surgeons and otolaryngologists. Few studies compare complication rates between these two specialties. We hypothesized that there would be no difference in the incidence of postoperative complications including recurrent laryngeal nerve (RLN) injury, hypocalcemia, or hematoma based on the surgical specialty performing the thyroidectomy. The 2016-2017 National Surgical Quality Improvement Program Targeted Thyroidectomy database was queried for patients who underwent thyroidectomy for both benign and malignant thyroid diseases. Thyroidectomies performed by general surgeons were compared to those performed by otolaryngologists. Multivariate logistic regression was used to identify risk factors associated with RLN injury, hematoma, and hypocalcemia. From 11,595 patients, 6313 (54.4%) were performed by general surgeons and 5282 (45.6%) by otolaryngologists. Goiter (43.7%) and nodule/neoplasm (40.8%) were the most common indications for the general surgery and otolaryngology cohorts respectively. General surgeons used an energy vessel sealant device more frequently (77.7% vs. 51.5%, p < 0.001), whereas RLN monitoring (67.4% vs. 58.3%, p < 0.001) and drain placement (44.3% vs. 14.8%, p < 0.001) were utilized more often by otolaryngology. After controlling for covariates, thyroidectomy by general surgeons had an increased associated risk of RLN injury (OR = 1.26, CI = 1.07-1.48, p = 0.006) and post-operative hypocalcemia (OR = 1.17, CI = 1.00-1.37, p = 0.046). Thyroidectomy volume is relatively equally distributed among general surgeons and otolaryngologists. Operation by a general surgeon is associated with an increased risk for RLN injury and postoperative hypocalcemia. This discrepancy may be explained by case volume, training, and/or completion of an endocrine surgery fellowship; however, this discrepancy still merits ongoing attention.