Background/Objectives: The accurate quantification of peripheral nerve axonal regeneration after injury is critically important. Current strategies are limited to detecting early reinnervation. DTI is an MRI modality permitting the assessment of fractional anisotropy, which increases with axonal regeneration. The aim of this pilot study is to evaluate DTI as a potential predictive factor of clinical outcome after median nerve section and microsurgical repair. Methods: We included 10 patients with a complete section of the median nerve, who underwent microsurgical repair up to 7 days after injury. The follow-up period was 1 year, including the current strategy with clinical visits, the Rosén-Lundborg score and electroneuromyography. Additionally, DTI MRI of the injured wrist was planned 1, 3 and 12 months post-operatively and once for the contralateral wrist. Results: The interobserver reliability of DTI measures was almost perfect (ICC 0.802). We report an early statistically significant increase in the fractional anisotropy value after median nerve repair, especially in the region located distal to the suture. Meanwhile, Rosén-Lundborg score gradually increased between the third and sixth month, and continued to increase between the sixth and twelfth month. Conclusions: DTI outcomes three months post-operation could offer greater predictability compared to current strategies. This would enable faster decision-making regarding the need for a potential re-operation in cases of inadequate early reinnervation.