The endodontic treatment of primary teeth is to maintain the function of the tooth free of symptoms until its physiological exfoliation. A critical factor for success is how quickly and effectively the root canal preparation can be performed. Therefore, the aim of this comparative in vitro study was to analyze the efficiency of two mechanical root canal preparation systems FM (FlexMaster) and HF (HyFlex EDM) to manual KF (K-file) on extracted primary molars. A total of 45 teeth were divided into three groups (n = 15): KF (#15-35), FM (04#30) and HF (25/~ OneFile). Root canal preparation was performed, and the preparation time was measured. All root canals were non-destructively analyzed by micro-computed tomography in the cervical, middle and apical thirds before and after preparation with regard to the parameters of canal transport (in μm) and centering ratio (0-1). Statistical analysis was performed at a 5% significance level using non-parametric tests. HF caused the lowest canal transport in the apical third (p = 0.008). The centering ratio value of HF was significantly higher in the middle third of the root canals than in the other two groups (p < 0.01). The mean instrumentation time was significantly higher for KF (6.67 min) than for FM (4.69 min) and HF (4.03 min, p < 0.01). HF can be recommended for primary molar root canal treatment.