Objectives: This study aimed to investigate the physical and emotional effects of the coronavirus disease 2019 pandemic in patients with fibromyalgia syndrome (FMS) and chronic low back pain (CLBP) patients.Patients and methods: The cross-sectional controlled study was performed with 1,360 participants (332 males, 1,028 females; mean age: 42.3 +/- 12.5 years; range, 18 to 65 years) between September 2020 and February 2021. The participants were evaluated in three groups: the FMS group (n=465), the CLBP group (n=455), and the healthy control group (n=440). Physical activity, pain levels, and general health status before and during the pandemic were evaluated in all participants. Stress levels were analyzed with the perceived stress scale (PSS) in all groups, and disease activity was analyzed with the fibromyalgia impact questionnaire (FIQ) in patients with FMS.Results: Patients with FMS had worsened general health status and pain levels during the pandemic compared to the other groups (p<0.01). The FMS group showed significantly higher PSS scores than those in other groups (p<0.01). There was a weak-positive correlation between FIQ and PSS parameters in patients with FMS (p<0.05, r=0.385).Conclusion: The general health status, pain, and stress levels of the patients with FMS and CLBP tended to worsen during the pandemic. This high-stress level appeared to affect disease activity in patients with FMS.