The behavioral effects of nasopharyngeal swab tests preceding dental treatment on pediatric dental patients has not been explored, particularly on uncooperative children planned for treatment with non-intravenous conscious sedation. The aim of this study is to assess the behavior effects of in-office SARS-CoV-2 nasopharyngeal swab testing on children and to determine the effects of the test on behavior for subsequent dental treatment. A retrospective chart review was conducted to identify children who had undergone swab testing followed by treatment with non-intravenous conscious sedation. Chi-square, Fisher’s exact and Wilcoxon tests were performed to analyze the effect of the swab on dental treatment. Linear regression was conducted to determine whether age, treatment duration, ASA status, non-intravenous conscious sedation medication, and gender affected behavior. Statistical significance was set at P<0.05. In total, 110 children (60 females, 50 males) were included in this study. The mean behavior scores were similar at swab testing and during treatment, for both males and females (P=0.16). Males demonstrated lower average behavior score compared to females during the swab (P<0.01) and dental treatment (P<0.02). In-office nasopharyngeal swab testing did not appear to produce a negative effect on patient behavior during the subsequent procedure appointment, although nasopharyngeal swab behavior was an independent predictor of behavior treatment behavior (P<0.02). Mean behavior scores were similar at swab testing and during dental treatment under sedation. Males demonstrated lower average behavior score compared to females during the swab and dental treatment.