Objective: Coronavirus disease-19 pandemic affected the whole world in 2020 and so far caused nearly 2 million deaths. The most commonly used method in the diagnosis of coronavirus disease-19 is to take swabs from specific areas in the upper respiratory tract, especially the nasopharynx. In this article, it was aimed to compare the effects of transoral/transnasal nasopharyngeal swab methods on anxiety score before and after the procedure. Methods: This study was designed as a prospective randomized clinical trial. Hundred and four volunteers between the ages of 18-65 were included in the study, and volunteers were divided into 2 groups. Transoral method was applied to group-1 and transnasal method was applied to group-2. Visual Analog Scale scoring was performed to measure the anxiety/pain/general discomfort levels of the participants before and after the procedure. Results: In this study, 50 volunteers from the transoral group and the rest 54 volunteers from the transnasal group, a total of 104 individuals were included. Before the procedure, no statistically significant difference in anxiety levels was observed between the groups. However, anxiety, pain, and general discomfort levels during the procedure were found to be lower in group 1. Conclusion: In the light of the results of our trial, we suggest that the transoral nasopharyngeal swab method can be a better alternative in selected patient groups. The prime advantage of this procedure is that it causes less pain and general discomfort. We think that many complications encountered in the transnasal method can be overcome by the transoral method.