Background and Objectives: Long-term outcomes of immediately postoperative rotational malreduction in the axial plane after operative treatment of supracondylar humeral fractures (SCHF) are unknown. This study aimed to investigate the long-term clinical outcomes and associated factors for immediately postoperative rotational malreduction of SCHF. Materials and methods: In this retrospective case–control study, 88 patients who underwent surgery for Gratland type III SCHF were enrolled between January 2012 and January 2020. Among them, 49 patients had immediately postoperative malrotational reduction (rotational malreduction group) and 39 patients had no rotational deformity (control group). To evaluate the associated factors for immediately postoperative rotational malreduction, demographic data, fracture patterns, physical examination signs, and preoperative radiological parameters were analyzed. To compare the clinical outcomes, operation time, range of motion of the elbow, time from operation to full range of motion, and Flynn criteria were evaluated. The Oxford elbow score was used to investigate long-term clinical outcomes for patients five years after operation. Results: The mean age was 5.7 ± 2.3 years and mean follow-up period was 15.7 ± 4.0 months. The rotational malreduction group had significantly more patients with oblique fracture pattern (p = 0.031) and Pucker sign (p = 0.016) and showed a significantly longer operative time (p = 0.029) than the control group. Although there was no significant difference in the range of elbow motion and the Flynn criteria, the Kaplan–Meier survival curve showed a longer time to recover the full range of elbow motion in the rotational malreduction group (p = 0.040). There were no significant differences in the long-term clinical outcomes assessed using the Oxford elbow score (p = 0.684). Conclusions: Oblique fracture pattern and Pucker sign may be associated with immediately postoperative rotational malreduction in the axial plane. Although patients with immediately postoperative rotational malreduction showed favorable results of long-term clinical outcomes, they required more weeks to recover the full range of elbow motion.