Background: Obesity and musculoskeletal pain are strongly related, but there is emerging evidence that body fat, not body weight, may be a better indicator of risk. There is, therefore, a need to determine if body fat is associated with musculoskeletal pain as it may improve management strategies. The aim of this systematic review was to investigate the association between body fat and musculoskeletal pain. Methods: Seven electronic databases were searched from inception to 8th January 2018. Cross-sectional and longitudinal studies investigating the association between measures of body fat and musculoskeletal pain were included. All included articles were assessed for methodological rigour using the Epidemiology Appraisal Instrument. Standardised mean differences (SMDs) and effect estimates were pooled for meta-analysis. Results: A total of 10,221 citations were identified through the database searching, which after abstract and full-text review, yielded 28 unique articles. Fourteen studies were included in the meta-analyses, which found significant cross-sectional associations between total body fat mass and widespread pain (SMD 0.49, 95% CI 0.37-0.61, p < 0.001). Individuals with low-back pain and knee pain had a higher body fat percentage than asymptomatic controls (SMD 0.34, 95% CI 0.17-0.52, p < 0.001 and SMD 0.18, 95% CI 0.05-0.32, p = 0.009, respectively). Fat mass index was significantly, albeit weakly, associated with foot pain (SMD 0.05, 95% CI 0.03-0.06, p < 0.001). Longitudinal studies (n = 8) were unsuitable for meta-analysis, but were largely indicative of elevated body fat increasing the risk of incident and worsening joint pain. There was conflicting evidence for an association between body fat percentage and incident low-back pain (3 studies, follow-up 4-20 years). Increasing knee pain (1 study) and incident foot pain (2 studies) were positively associated with body fat percentage and fat mass index. The percentage of items in the EAI graded as 'yes' for each study ranged from 23 to 85%, indicating variable methodological quality of the included studies. Conclusions: This systematic review and meta-analysis identified positive cross-sectional associations between increased body fat and widespread and single-site joint pain in the low-back, knee and foot. Longitudinal studies suggest elevated body fat may infer increased risk of incident and worsening joint pain, although further high-quality studies are required.