Introduction: Thorough treatment planning is essential for a good clinical outcome in orthognathic treatment. The planning is often digital. Both 2-dimensional (2D) and 3-dimensional (3D) software options are available. The aim of this randomized 2-arm parallel double-blinded active-controlled clinical trial was to comprae the outcomes of computer-based 2D and 3D planning techniques according to patient-reported health related quality of life. The hypothesis was that a 3D technique would give a better treatment outcome compared with a 2D technique. Methods: Orthognathic treatment for 62 subjects, aged 18 to 28 years, with severe Class III malocclusion was planned with both 2D and 3D techniques. After treatment planning but before surgery, the patients were randomly allocated via blind collection of 1 enveloped card for each subject in a 1:1 ratio to the test (3D) or the control (2D) group. Thus, the intervention was according to which planning technique was used. The primary outcome was patient-reported outcome measures. The secondary outcome was relationship between patient-reported outcome measures and cephalometric accuracy. Questionnaires on the patient's health-related quality of life (HRQoL) were distributed preoperatively and 12 months after surgical treatment. The questionnaires were coded, meaning blinding throughout the analysis. Differences between groups were tested with the Fisher permutation test. The HRQoL was also compared with measurements of cephalometric accuracy for the 2 groups. Results: Three subjects were lost to clinical follow-up leaving 57 included. Of these, 55 subjects completed the questionnaires, 28 in the 2D and 27 in the 3D groups. No statistically significant difference regarding HRQoL was found between the studied planning techniques: the Oral Health Impact Profile total showed -3.69 (95% confidence interval, -19.68 to 12.30). Consistent results on HRQoL and cephalometric accuracy showed a difference between pretreatment and postreatment that increased in both groups but to a higher level in the 3D group. A difference between pretreatment and posttreatment HRQoL was shown for both groups, indicating increased quality of life after treatment. This supports recent findings comparing 3D and 2D planning techniques. No serious harm was observed during the study. Conclusions: Improvements of HRQoL were shown after treatment independent of which planning technique, 2D or 3D, was used. No statistically significant difference was found between the planning techniques. Registration: This trial was not registered. Protocol: The protocol was not published before trial commencement.