Shoulder complex control of motion is influenced by neuromuscular function and can be quantified through the analysis of helical axes (HAs) dispersion. Muscle fatigue is a variable able to influence neuromuscular control, altering muscle activation timing and proprioception. The aim of the study was to describe shoulder complex HAs dispersion after muscle fatigue during upper limb movements of young healthy subjects. Thirty healthy right-handed volunteers (age 23.2 ± 2.6 years) were asked to perform a test made up of 15 humerothoracic flexion and rotation movements using both upper limbs in two different recording sessions. After each session, muscles of the tested movement were fatigued in isometric condition at dominant side. After fatigue, subjects repeated the test. Kinematics was recorded by an optoelectronic system and HAs dispersion was computed using Mean Distance (MD) and Mean Angle (MA) for the entire Range of Motion (RoM) and in portions of RoM. After fatigue of shoulder flexion muscles, greater MD (p = 0.001) and MA (p = 0.019) were found on the dominant side. After fatigue of shoulder rotation muscles, greater MD and MA were found on the dominant (p = 0.002 for MD; p = 0.047 for MA) and non-dominant (p = 0.038 for MD; p = 0.019 for MA) sides. Independently of fatigue, greater MA was found in portions of RoM with higher external resistance torque in flexion and rotation tasks. Muscle fatigue increases shoulder complex HAs dispersion, probably due to alteration in neuromuscular control. This data should be considered when exercise involving upper arms are proposed to subjects undergoing fatigue.