Background. Root canal treatment in primary teeth is quite difficult and time-consuming, especially canal preparation. Pain is the most common negative outcome following root canal treatment, occurring hours or days after treatment. It is an unpleasant experience for both the patient and the dentist. Objectives. The objective of this study was to assess the severity and duration of pain following the endo-dontic treatment of primary molars with the use of rotary and reciprocating preparation systems compared to the traditional manual method. Material and methods. The research sample consisted of 157 asymptomatic primary lower second molars with non-vital pulp that were indicated for root canal treatment. The patients were randomly divided into 3 groups: in the 1st group, the molars (n = 52) were prepared using the manual method; in the 2nd group (n = 53), a reciprocating automated preparation system (WaveOne®) was used; and in the 3rd group (n = 52), a rotary preparation system (ProTaper Next®) was used. Pain assessment was carried out after 6, 12, 24, 48, and 72 h, and after 1 week, using a four-face facial pain scale. Results. The manual method provided a higher pain score through 6, 12 and 24 h (p < 0.05) as compared to the 2 automated preparation systems. The intensity of pain did not vary between the 2 machine preparation systems after 6, 12, 24, and 48 h (p > 0.05). There were no differences between the 3 methods after 72 h and after 1 week (p > 0.05). Conclusions. The manual method caused more pain than the other 2 preparation systems, but there was no difference between the 2 automated methods. Automated root canal preparation systems could be used to reduce the intensity of postoperative pain after the endodontic treatment of primary teeth. © 2021 by Wroclaw Medical University.