Introduction: The objective of this 2-arm parallel trial was to compare the effects of direct and indirect bonding techniques on the orthodontic treatment process and outcomes. Methods: Thirty patients were randomly assigned to undergo bonding of brackets indirectly (group A, n = 15) or directly (group B, n = 15). Eligibility criteria included permanent dentition with bilateral Angle Class I molar and canine relationships, no previous orthodontic treatment, no skeletal discrepancy, and mild or moderate crowding. The main outcome was the orthodontic treatment results assessed using the American Board of Orthodontics Objective Grading System; the secondary outcomes were times taken to perform the laboratory and clinical steps, total treatment duration, plaque accumulation, formation of white spot lesions, bond failures, and need for additional archwire bending and bracket repositioning. The randomization sequence was created using an online randomization software. The patients were allocated with a 1:1 ratio using a block size of 4. The sequence generator was contacted by phone for group assignment after a patient was enrolled for allocation concealment. Blinding was implemented during the dental cast and radiographic evaluations, data entry, and data analysis. Patients were evaluated before treatment, and 1, 2, and 6 months after the start of treatment, and at the end of treatment. Results: All patients completed the study and were analyzed. There were no dropouts. Marginal ridge (median difference, -1.000; 95% confidence interval [CI], -2.99 to -0.001; P = 0.03) and total Objective Grading System scores (median difference, -3.999; 95% CI, -6.000 to -0.005; P = 0.03) were significantly higher in group B than in group A; other Objective Grading System categories did not differ significantly between the groups. The clinical time was significantly longer in group B than in group A (mean difference, -26.51; 95% CI, -29.57 to -23.46; P <0.001), and the total time was significantly longer in group A than in group B (mean difference, 19.03; 95% CI, 15.32 to 22.74; P <0.001). There were no significant between-group differences in treatment duration, plaque accumulation, formation of white spot lesions, bond failure, or need for additional archwire bending or bracket repositioning. No harms were encountered. Conclusions: Indirect bonding was significantly faster than direct bonding in the clinical stage and yielded better marginal ridge and total scores. Both techniques showed similar rates of plaque accumulation, formation of white spot lesions, bond failure, and additional archwire bending and bracket repositioning.