Background: This study aimed to clarify trunk muscle activity during jump header shooting and examine the immediate effects of trunk stabilization exercises on trunk muscle activity. Methods: Nineteen male college students who had played soccer in junior high and high school clubs and youth sports teams for over 5 years were assigned to either the trunk stabilization exercise group (n = 10) or the control group (n = 9). Muscle activity during jump header shooting was measured before and after intervention. The intervention in the trunk stabilization exercise group was trunk muscle training, whereas that in the control group was sitting. The phases of jump header shooting and the effects of the interventions were compared. Results: The internal oblique activity during the push-off phase and early floating phase was significantly greater than that during the late floating phase. The muscle activity of the internal oblique increased from the push-off phase, prior to the increase in muscle activity of the rectus abdominis and external oblique, whereas the muscle activity of all abdominal muscles increased immediately after take-off. The trunk stabilization exercise intervention decreased the muscle activity of the erector spinae during jump header shooting. Conclusions: These results provide useful coaching-related insights for jump header shooting.