Purpose: The radiation-free, noninvasive and computer-assisted Spinal Mouse® (SM) is a reliable and valid measuring instrument for functional analysis of the pediatric spine. The aim of this study was to examine the intra-rater reliability of the SM measurements in children with cerebral palsy (CP) and to investigate differences after a 1 week of the rehabilitation program. Methods: A total of 168 SM investigations in the sagittal plane and frontal plane at three measurement times from a sample of 28 children (n = 10 girls, age 9.7 ± 3.1 years) with CP were eligible for evaluation. For the verification of reliability, the measurement results from the first and second measurement times (t1, t2) were used at intervals of 1 day. In addition, differences after the rehabilitation program the patients underwent (t3) were evaluated using the measurement results of the first and third measurements (5-day interval). Results: The results show good to excellent intra-rater reliability for the SM measurements, both in the sagittal and in the frontal plane (ICC values = 0.69–0.99). Furthermore, significant changes may occur after only 1 week of therapeutic intervention for total spinal inclination (t1: 12.82 ± 5.40, t3: 11.11 ± 5.60, p = 0.014, Cohen’s d = 0.43) and spine length (t1: 401.75 ± 69.05, t3: 409.25 ± 63.58, p = 0.030, Cohen’s d = 0.43). Conclusions: SM can be used to generate reliable values for functional analysis of the spine in children with CP. Furthermore, significant posture differences can be demonstrated by therapeutic interventions, especially in the spine inclination (Inc) and spine length (SL). Graphic abstract: These slides can be retrieved under Electronic Supplementary Material.[Figure not available: see fulltext.].