Previous studies have reported that glenohumeral internal rotation deficit (GIRD) may increase the risk of shoulder injury. However, the effects of GIRD on baseball pitching among pitchers of different age groups are still unclear. The study participants were 24 high school and 24 university pitchers. For each age group, the pitchers were evenly divided into a GIRD group and a normal group. The pitching motion of each participant was captured using a motion analysis system at a sampling frequency of 300 Hz. The kinematics and kinetics of the throwing shoulder and trunk were quantified, and statistical differences between the groups were examined by 2-sample t tests. For both age groups, significant differences were observed in shoulder external rotations of the GIRD and normal groups. Compared with the university pitchers in the normal group, the university pitchers with GIRD exhibited a greater shoulder loading and did more internal rotation work in the acceleration phase. The high school pitchers with GIRD showed a larger trunk tilt and less trunk rotation than the university pitchers with GIRD. However, the university pitchers with GIRD exhibited a larger shoulder posterior force and horizontal adduction torque than the high school pitchers with GIRD. Pitchers with GIRD do change their pitching motions, and the greater resulting shoulder joint loading predisposes them to a greater risk of shoulder injury, especially among university pitchers.