Background: Musculoskeletal disorders such as osteoarthritis, chronic low back pain, radicular syndromes and osteoporosis produce major clinical burdens, and noninvasive therapies capable of reaching deep anatomical structures are increasingly needed. Nuclear magnetic resonance therapy (molecular biophysical stimulation therapy; NMRT MBST) applies resonance-based magnetic fields to deliver uniform biophysical stimulation independent of tissue depth. This review synthesizes clinical and mechanistic evidence to evaluate the therapeutic potential of NMRT MBST and contextualize it within emerging deep-tissue biophysical treatment strategies. Methods: A systematic search of PubMed, Ovid Embase and peer-reviewed, published reviews identified 15 studies, including randomized trials, imaging investigations, observational cohorts, long-term follow-ups and blinded veterinary work. Experimental literature examining cellular, metabolic and molecular responses to NMRT MBST was reviewed to align biological effects with clinical outcomes. Results: NMRT MBST is consistently reported as safe, with no treatment-emergent adverse events. Clinical findings indicate improvements in pain, function and, in selected studies, imaging or densitometric parameters across osteoarthritis, spine-related pain, radicular syndromes and osteoporosis. Placebo-controlled effects were demonstrated in finger-joint osteoarthritis and radicular pain, while one robust knee osteoarthritis trial showed no short-term superiority over placebo. Mechanistic studies have shown anti-inflammatory, mitochondrial, redox, anabolic, neurotrophic, epigenetic and circadian effects that closely parallel near-infrared photobiomodulation, supporting the concept of NMRT MBST as a deep-penetrating analogue capable of reaching tissues inaccessible to light. This positions NMRT MBST within a broader therapeutic framework in which biophysical stimulation may modulate metabolic–inflammatory–regenerative axes in deep musculoskeletal and central nervous system (CNS) structures. Conclusions: NMRT/MBST appears to be a safe and biologically coherent deep-tissue biophysical therapy with promising clinical effects. Larger trials, optimized dosing, mechanistic biomarkers and head-to-head comparisons with established modalities are needed to define its therapeutic role and to clarify how deep-acting biophysical interventions may be integrated into future musculoskeletal and CNS care.