The aim of this study is to evaluate the course of the treatment and clinical and functional outcomes of femur lengthening in adolescents with congenital disorders by the application of different surgical methods. This retrospective study comprised 35 patients (39 procedures). A total of 11 patients underwent femur lengthening with the use of the intramedullary magnetic nail (IMN) Precise 2 (NuVasive, San Diego, CA, USA), 7 patients (11 procedures) with the use of the monolateral external distractor Modular Rail System (MRS) (Smith and Nephew, Memphis, TN, USA), and 17 with the use of the computer-assisted external fixator Taylor Spatial Frame (TSF) (Smith and Nephew, Memphis, TN, USA). The inclusion criteria were as follows: (1) congenital femoral length deficiency without any axial deformities and (2), independently of the finally applied treatment, the technical possibility of use of each of the analyzed methods. The distraction index did not differ significantly between the groups (p = 0.89). The median lengthening index was the lowest in the IMN group (24.3 d/cm; IQR 21.8–33.1) and statistically different in comparison to the MRS (44.2 d/cm; IQR 42–50.9; p < 0.001) and the TSF groups (48.4 d/cm; IQR 38.6–63.5; p < 0.001). Similarly, the consolidation index in the IMN group (12.9 d/cm; IQR 10.7–21.3) was statistically lower than that in the MRS (32.9 d/cm; IQR 30.2–37.6; p < 0.001) and the TSF (36.9 d/cm; IQR 26.6–51.5; p < 0.001) groups. This study indicates that IMN is a more valuable method of treatment for femoral length discrepancy without axial deformity than MRS and TSF in complication rate and indexes of lengthening and consolidation.