The aim of this trial was to evaluate and compare perceived pain, discomfort, and jaw function impairment between orthodontic treatments combined with skeletal anchorage and treatment using conventional anchorage with headgear or transpalatal bar. A total of 120 adolescent patients in order to start orthodontic treatment were consecutively recruited and randomized into three groups with different anchorage. Group A underwent installation of a skeletal anchorage (Onplant or Orthosystem implant), group B received headgear, and group C a transpalatal bar. Questionnaires were used to assess pain intensity, discomfort, analgesic consumption, and jaw function impairment from baseline to the end of treatment. Pain scores overall peaked on day 2 and were almost back to baseline on day 7. The site with the highest pain scores during treatment was incisors in contact but with no differences between groups. Pain intensity from molars was significantly less in the skeletal anchorage group A compared to the transpalatal bar group C the first 4 days in treatment and with no sign differences compared to headgear. The results confirm that there were very few significant differences between patients’ perceptions of skeletal and conventional anchorage systems during orthodontic treatment. Consequently, these new appliances were well accepted by the patients in a long time perspective and can thus be recommended.