This study aimed to validate the use of grayscale muscle ultrasound by measuring echo intensity to longitudinally evaluate functional muscle reinnervation in a rabbit peroneal nerve defect model. Eighteen New Zealand White rabbits underwent a 30-mm peroneal nerve reconstruction with autografts or decellularized allografts. Ultrasound measurements of tibialis anterior muscles were performed before surgery and at 4, 8, 12, 16, 20, and 24 weeks postoperatively and included cross-sectional muscle area, mean gray value (MGV), and mean gray value normalized for area (MGVA). At 24 weeks, functional motor recovery was evaluated with isometric tetanic force (ITF) and compound muscle action potential (CMAP). MGVA data was compared with ITF and CMAP measurements by calculating the Spearman correlation coefficient. Muscle area (Left/Right Ratio (L/R)) of autografts was superior to allografts at 4, 12, 16, 20 and 24 weeks (p<0.03 for all comparisons). MGVs of the operated side were significantly higher for autografts at 4, 8, and 12 weeks and at 12, 16, 20, and 24 weeks for allografts (p<0.01 for all comparisons), compared to their unoperated sides. Similar patterns were seen in both groups for MGVA (operated versus control side). MGVA (L/R) demonstrated a strong correlation with ITF (L/R) for autografts (ρ = -0.7) and allografts (ρ = -0.87), but inconsistent with CMAPs (L/R). Quantitative muscle ultrasound demonstrated a reliable, non-invasive tool for evaluating motor recovery in a rabbit peroneal nerve reconstruction model. Clinical translation could provide valuable insights into muscle health and structural changes following nerve reconstruction.