Background: s: Pain management is one of the most important factors affecting the success of pediatric dentistry. Therefore, new needle- and pain-free local anesthesia techniques have been developed in parallel with technological advancements. The purpose of this study is to compare the pain perception and dental anxiety levels associated with a needle-free injection system (Comfort-in TM ) and the classic needle method during treatment-required infiltration anesthesia in children. Methods: This randomized controlled crossover split-mouth clinical study included 94 children who required dental treatment with local anesthesia using a dental needle or needle-free injection system for the bilateral primary molars. The Wong-Baker Scale (WBS) was used to measure pain perception at different times, and the Modified Child Dental Anxiety Scale (MCDAS) was used to measure the anxiety level of the child. A statistical software package was used to process the data. Statistical significance was set at P < 0.05. Results: There was no significant difference between the needle-free injection system and dental needle method during the induction stage for filling and pulpotomy (P > 0.05). “Pain on postoperative 1st day” was similar in both types of anesthesia (P = 0.750). Conclusions The needle-free injection system was as effective as the dental needle method. The Comfort-in TM system was an acceptable alternative for patients during the postoperative period. Understanding how pain management may be provided during local anesthesia administration and a child’s fear and anxiety regarding the dentist may lead to better dental compliance.