Background: Various root canal filling materials for primary teeth have been used from time to time; the most commonly used and readily available materials are zinc oxide eugenol and Vitapex. Aim: We conducted this study with the aim of comparing the effect of Zinc oxide eugenol and Vitapex for carrying out endodontic therapy of necrotic primary teeth. Methods: Study was performed on 165 teeth. Clinical and radiographic assessment of the patients was done pre-operatively. In the zinc oxide eugenol group, paste was prepared and paper points covered with the material were used to coat the root canal walls. In the Vitapex group, the premixed paste was packaged in a syringe with a number of disposable tips. Results: On pre-operative clinical and radiographic assessment of 165 teeth, pain was found among 116 (70.3%), bone radiolucency 90 (54.5%), abnormal mobility 75 (45.5%) subjects. Swelling outside the oral cavity was seen in least 31 (18.8%) number of subjects. Among subjects in which Zinc oxide eugenol was used, 31 (18.8%) subjects showed short fillings while in cases where Vitapex was used, 9.7 percent showed short fillings. Conclusion: Premixed calcium hydroxide and iodoform paste (Vitapex) offered as a healthy choice as a filling material following pulpectomy in primary non-vital teeth as compared to zinc oxide eugenol.