Cerebral palsy (CP) is a common reason for human motor ability limitations caused before birth, through infancy or early childhood. Poor head control is one of the most important problems in children with level IV CP and level V CP, which can affect many aspects of children’s lives. The current visual assessment method for measuring head control ability and cervical range of motion (CROM) lacks accuracy and reliability. In this paper, a HeadUp system that is based on a low-cost, 9-axis, inertial measurement unit (IMU) is proposed to capture and evaluate the head control ability for children with CP. The proposed system wirelessly measures CROM in frontal, sagittal, and transverse planes during ordinary life activities. The system is designed to provide real-time, bidirectional communication with an Euler-based, sensor fusion algorithm (SFA) to estimate the head orientation and its control ability tracking. The experimental results for the proposed SFA show high accuracy in noise reduction with faster system response. The system is clinically tested on five typically developing children and five children with CP (age range: 2–5 years). The proposed HeadUp system can be implemented as a head control trainer in an entertaining way to motivate the child with CP to keep their head up.