Aim: To evaluate voids and sealing ability using a disposable syringe, endodontic pressure syringe, and Skinni syringe with NaviTip in primary molars with cone-beam computed tomography (CBCT). Materials and methods: The 15 extracted primary mandibular molars with at least one root ≥8 mm length and an equal number of mesiobuccal canals were divided into three groups, i.e., obturation using a disposable syringe, an endodontic pressure syringe, and a Skinni syringe with NaviTip, respectively. The evaluation of the apical seal was determined as the measurement between the apical end of the filling material and the radiographic apex. The quality of the filling was determined by the size, number, type, and location of voids present. Statistical analysis was done using the Chi-square test and post-hoc test. Results: The endodontic pressure syringe score was the highest and statistically significant in obtaining apical seal (p = 0.013). Disposable syringe shows highest size of voids (p = 0.01) in which type I-voids (p = 0.04) and type S-voids (p = 0.07) were statistically significant. The location of voids was maximum at the middle third of the root (p = 0.016). Conclusion: The endodontic pressure syringe provided the best root canal obturation of primary molars, whereas the disposable syringe was least effective with the maximum number and size of voids. Clinical significance: Comparing the voids and sealing abilities of different obturating techniques with CBCT would help the pediatric practitioners for better outcome of obturation in primary teeth.