The cross-sectional and longitudinal associations between pain-related factors and muscle activity in patients with chronic low back pain (CLBP) are unclear. This study aimed to examine the temporal associations between them in a CLBP patient using a single-case analysis to account for an individual course.A patient with a history of lower back pain lasting more than 3 months was studied from March 16, 2020 to May 30, 2020. Surface electromyographic signals were recorded from over the bilateral lumbar erector spinae in the patient while performing a standing trunk flexion and re-extension task. The average value for muscle activity during each movement phase was estimated, and the flexion relaxation ratio (FRR) of all channels was subsequently calculated. Pain-related factors and disability were assessed using questionnaires. All assessments were performed nine times, along with 2-3 months of intervention. Once or twice per week, the patient received physical therapy that consisted of soft tissue mobilization, joint mobilization, nerve mobilization, and patient education. A cross-lag correlation analysis of this single case was conducted.Pain-related factors showed a trend toward improvements in all variables when compared to those in the first assessment; however, there was no general change (increase) in FRR over time. The cross-lag correlation analysis revealed that improvements in FRR were associated with improvements in body perception disturbance (ρ = -0.78, p < 0.01), and that improvements in muscle activity during the extension phase were associated with improvements in pain (ρ = 0.75), psychological factors (ρ = 0.57), and disability (ρ = 0.67) (p < 0.05).Our findings suggest that improvements in body perception were temporally associated with improvements in FRR, and improvements in pain, psychological factors, and disability were temporally associated with a reduction in muscle activity during the trunk extension phase in this patient with CLBP.