Inertial sensor technology has assumed an increasingly important role in the field of human motion analysis. However, the reliability of the kinematic estimates could still be critical for specific applications in the field of functional evaluation and motor rehabilitation. Within this context, the definition of subject-specific multi-body kinematic models is crucial since it affects the accuracy and repeatability of movement reconstruction. A key step for kinematic model calibration is the determination of bony segment lengths. This study proposes a functional approach for the in vivo estimation of the humerus length using a single magneto-inertial measurement unit (MIMU) positioned on the right distal posterior forearm. The humerus length was estimated as the distance between the shoulder elevation axis and the elbow flexion-extension axis. The calibration exercise involved five shoulder elevations in the sagittal plane with the elbow completely extended and five elbow flexion-extensions with the upper arm rigidly aligned to the trunk. Validation of the method was conducted on five healthy subjects using the humerus length computed from magnetic resonance imaging as the gold standard. The method showed mean absolute errors of 12 ± 9 mm, which were in the estimate of the humerus length. When using magneto-inertial technology, the proposed functional method represents a promising alternative to the regressive methods or manual measurements for performing kinematic model calibrations. Although the proposed methodology was validated for the estimation of the humerus length, the same approach can be potentially extended to other body segments.