BACKGROUND: Myofascial pain syndrome (MPS), a chronic musculoskeletal disorder characterized by myofascial trigger points (MTrPs), causes localized pain and dysfunction. The objective is to compare the immediate therapeutic effects of low-intensity focused ultrasound (LIFU) versus low-intensity planar ultrasound (LIPU) on pain and function in upper trapezius MPS. METHOD: This study was designed as a single-blind, randomized controlled trial. The patients (20 ≤ aged ≤ 70) diagnosed with MPS of the upper trapezius were randomly allocated to either LIFU (study group; n = 20; 9 men, 11 women) or LIPU (control group; n = 20; 15 men, 5 women) treatments (1.5 W/cm, 1 MHz, 5 min, once a day, 3 days). The primary outcome was pain severity, assessed immediately post-treatment using the Visual Analog Scale (VAS; 0 ~ 10 cm), and served as the central efficacy endpoint. Secondary outcomes comprised supplemental assessments including: (1) multidimensional pain characterization via the Short-Form McGill Pain Questionnaire (SF-MPQ); (2) functional disability quantification through the Neck Disability Index (NDI); and (3) neuromuscular biomarkers measured by surface electromyography (sEMG) parameters (root mean square [RMS], median frequency [MF]). The outcomes were assessed before treatment and 10 min, 72 h after completing the third and final session of treatment. RESULTS: Pain intensity, as measured by the VAS, decreased significantly immediately after treatment in both the LIFU group (median difference [MD] = -2.0 cm; 95% confidence interval [CI]: -2.5 to -1.5 cm; p = 0.002) and the LIPU group (MD = -1.0 cm; 95% CI: -1.5 to -0.5 cm; p = 0.001), with these reductions maintained at 72 h post-treatment. Both SF-MPQ and NDI scores showed significant improvements following treatment in both groups. A significant reduction in RMS parameters was observed in the LIPU group immediately after treatment (MD = -15.3 µV; 95% CI: -20.0 to -10.5 µV; p = 0.028). No significant differences were observed between the groups in terms of pain alleviation, functional improvement, and alterations in neuromuscular electrophysiological activity (p > 0.05); however, moderate to large effect sizes suggest possible clinical relevance. No adverse events were reported. CONCLUSION: Both LIFU and LIPU can be considered effective therapeutic options, offering immediate symptom relief in patients with upper trapezius MPS. TRIAL REGISTRATION: The protocol was registered at the Chinese Clinical Trial Register (ChiCTR2500097431) as a clinical trial on 19/02/2025 http://www.chictr.org.cn/ .