Background: Animal models are one of the first steps in translation of basic science findings to clinical practice. For tendon healing research, transgenic mouse models are important to advance therapeutic strategies. However, the small size of the structures complicates surgical approaches, histological assessment, and biomechanical testing. In addition, available models are not standardized and difficult to compare. How surgery itself affects the healing outcome has not been investigated yet. The focus of the study was to develop a procedure that includes a transection and microsurgical reconstruction of the Achilles tendon but, unlike other models, preserves the sciatic nerve. We wanted to examine how distinct parts of the technique influenced healing. Methods: For this animal model study, we used 96 wild-type male C57BL/6 mice aged 8–12 weeks. We evaluated different suture techniques and macroscopically confirmed the optimal combination of suture material and technique to minimize tendon gap formation. A key element is the detailed, step-by-step illustration of the surgery. In addition, we assessed histological (Herovici and Alcian blue staining) outcome parameters at 1–16 weeks postoperatively. Microcomputed tomography (micro-CT) was performed to measure the bone volume of heterotopic ossifications (HOs). Biomechanical analyses were carried out using a viscoelastic protocol on the biomechanical testing machine LM1. Results: A modified 4-strand suture combined with a cerclage for immobilization without transection of the sciatic nerve reliably eliminated gap formation. The maximal dorsal extension of the hindlimb at the upper ankle joint from the equinus position (limited by the immobilization cerclage) increased over time postoperatively (operation: 28.8 ± 2.2°; 1 week: 54 ± 36°; 6 weeks: 80 ± 11.7°; 16 weeks: 96 ± 15.8°, p > 0.05). Histological staining revealed a maturation of collagen fibres within 6 weeks, whereas masses of cartilage were visible throughout the healing period. Micro-CT scans detected the development of HOs starting at 4 weeks and further progression at 6 and 16 weeks (bone volume, 4 weeks: 0.07604 ± 0.05286 mm3; 6 weeks: 0.50682 ± 0.68841 mm3; 16 weeks: 2.36027 ± 0.85202 mm3, p > 0.001). In-depth micro-CT analysis of the different surgical elements revealed that an injury of the tendon is a key factor for the development of HOs. Immobilization alone does not trigger HOs. Biomechanical properties of repaired tendons were greatly altered and remained inferior 6 weeks after surgery. Conclusion: With this study, we demonstrated that the microsurgical technique greatly influences the short- and longer-term healing outcome. When the sciatic nerve is preserved, the best surgical reconstruction of the tendon defect is achieved by a 4-strand core suture in combination with a tibiofibular cerclage for postoperative immobilization. The cerclage promotes a gradual increase in the range of motion of the upper ankle joint, comparable with an early mobilization rehabilitation protocol. HO, as a key mechanism for poor tendon healing, is progressive and can be monitored early in the model. The translational potential of this article: The study enhances the understanding of model dependent factors of healing. The described reconstruction technique provides a reproducible and translational rodent model for future Achilles tendon healing research. In combination with transgenic strains, it can be facilitated to advance therapeutic strategies to improve the clinical results of tendon injuries.