Depression is a relevant risk factor for low back pain and is associated with the outcomes of low back pain. Depression also often overlaps with somatisation. As previous studies have suggested that somatisation or a higher somatic symptom burden has a role in the outcomes of low back pain, the aim of the present cross-sectional study was to examine whether somatic symptom burden was associated with health-related quality of life in individuals with chronic low back pain independent of depression. We analyzed internet survey data on physical and mental health in Japanese adults aged 20–64 years with chronic low back pain (n = 3,100). Health-related quality of life was assessed using the EuroQol five dimensions (EQ-5D) questionnaire. Somatic symptom burden and depression were assessed using the Somatic Symptom Scale-8 (SSS-8) and the Patient Health Questionnaire-2 (PHQ-2), respectively. SSS-8 score was categorized as no to minimal (0–3), low (4–7), medium (8–11), high (12–15), and very high (16–32). The association between SSS-8 and EQ-5D was examined using linear regression models, adjusting for depression and other covariates, including age, sex, BMI, smoking, marital status, education, exercise, employment, and the number of comorbid diseases. A higher somatic symptom burden was significantly associated with a lower health-related quality of life independent of depression and the number of comorbid diseases (regression coefficient = 0.040 for SSS-8 high vs. very high and 0.218 for non to minimal vs. very high, p trend <0.0001). In conclusion, somatic symptom burden might be important for the health-related quality of life of individuals with chronic low back pain.