Objective: To assess the accuracy of bracket positioning using two different materials for the construction of indirect bonding trays. Materials and Methods: A randomized controlled trial was conducted on 20 patients (200 brackets) divided into two groups. Group A used indirect bonding trays made of transparent flexible silicone (Memosil 2), while Group B used trays made of double-layer thermoformed sheets. Upper teeth (from right to left second premolars) were bonded, excluding molar tubes. Virtual bracket positioning was performed using digital scans and 3D-printed models. Post-bonding accuracy was evaluated by superimposing pre- and post-treatment models and measuring deviations in vertical (occluso-gingival) and horizontal (mesio-distal) directions. Results: Thermoformed trays demonstrated superior vertical accuracy compared to silicone trays. Conversely, silicone trays showed better horizontal accuracy. All measured deviations were clinically acceptable (<0.5 mm). Statistical analysis revealed significant differences between the groups (p < 0.05). Conclusion: The choice of tray material influences bracket positioning accuracy, with thermoformed trays excelling in vertical precision and silicone trays performing better horizontally. Clinicians should consider these trade-offs when selecting tray materials for indirect bonding. Digital workflows enhance reproducibility, supporting their adoption in orthodontic practice.