Botulinum neurotoxin type A (BoNT-A) is widely used to reduce spasticity in children with cerebral palsy. Despite its therapeutic benefits, incomplete muscle recovery has been observed post-treatment. This study evaluated longitudinal BoNT-A effects on muscle morphology over one year in children with CP (n = 26, mean age: 5.19 years ± 3.26). Three-dimensional freehand ultrasound assessed medial gastrocnemius muscle volume (MV), muscle belly length (ML), cross-sectional area (CSA), and echo intensity (EI) at baseline and at 3, 6, and 12 months post-BoNT-A. Z-score normalization accounted for natural muscle growth. Linear mixed models analyzed muscular changes over time, and repeated-measures ANOVA compared muscle parameters to an age- and severity-matched control group (n = 26, mean age: 4.98 ± 2.15) at one-year follow-up. MV exhibited a declining trend at 3 (p = 0.005), 6 (p = 0.003), and 12 months (p = 0.007), while ML remained unchanged throughout follow-up (p = 0.95). The initially reduced CSA at 6 months (p = 0.0005) recovered at one year, and EI increased only at 3 months post-BoNT-A (p < 0.0001). At one-year follow-up, there was a trend for reduced growth rate (MV/month) (p = 0.035) in the intervention group, whereas the control group exhibited an increased muscle growth (p = 0.029). These findings suggest distinct recovery timelines for CSA and ML, which may explain the incomplete MV recovery and highlight substantial interindividual variation in recovery processes.