Background: Myofascial trigger points (MTrPs) are hyperirritable spots in skeletal muscle associated with pain and dysfunction, often impacting individuals’ quality of life. Various interventions, such as dry needling and manual therapy, have shown limited effects in addressing these conditions. This study aimed to assess the effectiveness of a functional neurology intervention in reducing pain and improving muscle function in patients with MTrPs in the upper trapezius muscle. We hypothesized that a single session of functional neurology intervention would significantly increase the pressure pain threshold (PPT) and improve peripheral vascular response in individuals with myofascial trigger points compared to a control group. Methods: A randomized controlled trial (RCT) was conducted with 63 participants randomly assigned to an experimental (receiving functional neurology treatment) or control group. Pre- and post-treatment assessments were conducted, and both intra- and inter-group comparisons were performed using algometry to measure the PPT and infrared thermography to analyze peripheral vascular response. Data were analyzed using dependent and independent t-tests with statistical significance set at p < 0.05. Results: The experimental group demonstrated a significant 46.4% increase in PPT, while the control group showed negligible changes. Thermographic analysis indicated improved peripheral blood flow in the experimental group, reflected by increased skin temperatures and reduced thermal anomalies. No significant differences were observed between the groups at baseline. Conclusions: A single session of functional neurology intervention significantly reduced pain and improved muscle function in patients with MTrPs. These findings suggest that functional neurology offers a promising non-invasive alternative to traditional treatments, with potential implications for more rapid and sustained therapeutic outcomes.