Postoperative swallowing, affected by general anesthesia and intubation, plays an important part in airway and oral intake safety regarding effective oropharyngeal and esophageal emptying. However, objective evidence is limited. This study aimed to determine the time required from emergence to effective oropharyngeal and esophageal emptying in patients undergoing non-intubated (N) or tracheal-intubated (I) video-assisted thoracoscopic surgery (VATS). Hyoid bone displacement (HBD) by submental ultrasonography and high-resolution impedance manometry (HRIM) measurements were used to assess oropharyngeal and esophageal emptying. HRIM was performed every 10 min after emergence, up to 10 times. The primary outcome was to determine whether intubation affects the time required from effective oropharyngeal to esophageal emptying. The secondary outcome was to verify if HBD is comparable to preoperative data indicating effective oropharyngeal emptying. Thirty-two patients suitable for non-intubated VATS were recruited. Our results showed that comparable HBDs were achieved in all patients after emergence. Effective esophageal emptying was achieved at the first HRIM measurement in 11 N group patients and 2 I group patients (p = 0.002) and was achieved in all N (100%) and 13 I group patients (81%) within 100 min (p = 0.23). HBD and HRIM are warranted for detecting postoperative oropharyngeal and esophageal emptying.