The objective of this study was to investigate morphological and physiological characteristics of painful muscles in women with (MYA, n= 42) and without (CON, n = 20) trapezius myalgia, and assess changes in response to a 10-week, randomized, controlled trial. MYA accomplished: (1) specific strength training (SST); (2) general fitness training (GFT); or (3) reference intervention (REF). Differences in muscle morphology could not be detected by ultrasound imaging. Significantly lower pressure pain threshold (PPT) and shoulder torque were observed for MYA, indicating pain-related lack of full activation. After 10 weeks, increased shoulder torque and PPT of the painful trapezius were observed in SST solely. The PPT of a pain-free reference muscle was increased in response to both SST and GFT, indicating a general effect of physical activity on pain perception. This study shows clinically relevant improvement in pain sensitivity and muscle strength capacity in response to SST.