Aim: To investigate the corticomotor projection to the upper limb in children with hemiplegic cerebral palsy (CP) and the changes that occur with botulinum toxin (BTX)-A. Methods: The study design is a pilot prospective randomized trial. Twenty-two children with hemiplegic CP aged 7 years to 13 years 11 months were recruited. Treatment group (12) received one series of BTX-A injections into the upper limb. Control group (10) did not receive upper limb BTX-A. All participants except one treatment group participant also received lower limb BTX-A. Transcranial magnetic stimulation (TMS) was performed at baseline, and 1, 3 and 6 months post-injection. Outcome measures were: change in position of affected and unaffected side first dorsal interosseous optimal site of stimulation (OPTx). Results: A shift in affected and unaffected side OPTx was observed for both treatment and control groups, and there was no statistically significant difference between groups at 1, 3 or 6 months. Poor tolerance of TMS cortical stimuli > 80% was observed. Conclusion: Corticomotor projections associated with the upper limb in children with hemiplegic CP show significant variability over a 6-month period. This variability may reflect central motor reorganization because of systemic BTX-A effect or developmental changes. Upper limb BTX-A therapy is associated with reorganization of both affected and unaffected projections. Poor tolerance of the TMS procedure, in conjunction with higher cortical thresholds, may limit the usefulness of TMS as an investigatory tool in young children with movement disorders.