The aim of this study was to evaluate the post-discharge effects of oral midazolam with intranasal fentanyl sedation in pediatric patients who had dental treatment and to evaluate parents’ preference regarding sedation visits. Methods: A total of 32 uncooperative healthy pediatric patients aged 3–6 years old who met the inclusion criteria were included. In the first visit, one group received oral midazolam (0.7 mg/kg) with intranasal fentanyl (1 μg/kg) sedation (M/F) and the other group received oral midazolam with intranasal placebo (M), and in the second visit each group received the other type of sedation in a cross-over type. In this cross-sectional study, a post-discharge phone-call questionnaire was carried out 24 hours after both sedation visits with the parents to evaluate the children's behavior, function, balance, eating pattern, sleeping pattern, vomiting incidents, and any possible side effects, as well as parents’ satisfaction and preference. The Wilcoxon signed-rank test was used to analyze the categorical variables, and the Chi-square test was performed to analyze the parents’ preference. Result: A total of 32 parents responded to the phone-call questionnaire after 64 sedation visits. All of them were mothers. There was no statistically significant difference between the two groups with respect to recovery to normal function and balance, behavior, incidents of fever, vomiting, sleep disturbance, oversleeping, and adverse behavioral changes (p > 0.05). Children required a significantly longer amount of time until the first meal after M/F sedation (p = 0.04). No significant difference was found between parents’ preferences regarding the sedation visits (p > 0.05). Conclusion: Intranasal fentanyl added to oral midazolam sedation could have an effect on post-discharge adverse behavioral changes, prolonged sleeping, and prolonged recovery time. Children sedated with midazolam/ fentanyl required a longer amount of time until the first meal. Vomiting and fever occurred similarly in both sedation regimens with a low incidence. There was no difference in parents’ preferences regarding the two sedation regimens.