Manipulative therapy (MT) is a therapy in which a judo therapist manually rubs, presses, or taps the musculoskeletal system. MT is considered a cost-effective physical therapy that noninvasively promotes blood flow, relieves pain, and improves muscle flexibility. However, very few studies have evaluated the effectiveness of MT using objective measures in comparison with other medical fields; moreover, consistent results have not been obtained. In this study, we evaluated the upper trapezius muscles of 36 young adults using diffuse correlation spectroscopy (DCS) and a digital palpation system (Myoton Pro) to examine the effects of MT on local blood flow and stiffness. DCS is a new tissue blood flow measurement technique that can measure dynamic local blood flow in deeper tissue noninvasively using near-infrared light. Myoton Pro is a commercially available digital palpation system that can quantitatively evaluate muscle stiffness. A 5-min MT session significantly increased the blood flow by approximately 2-fold on the treated side, and the effects lasted 20 min. Additionally, muscle stiffness decreased on the treated side, while no change was observed on the untreated side, indicating the clinical benefits of MT in enhancing blood flow and promoting mobility. The results also demonstrated that the greater the initial stiffness of the patient’s muscle, the more effective MT was in reducing muscle stiffness. Although not statistically significant, a correlation trend was observed between the relative increase in blood flow and the decrease in stiffness of the treated muscle, suggesting a relationship between the effects of MT on blood flow and the relaxation of muscle tone.