Obesity is associated with numerous chronic diseases, including musculoskeletal (MSK) pain, which affects on quality of life (QoL). There is, however, limited research providing a comprehensive MSK pain profile of an obese cohort. This retrospective study used a patient database at a national weight management service. After ethical approval, anonymized patient data were statistically analyzed to develop a pain profile, investigate relationships between pain, sleep, and function, and explore variables associated with having low back pain (LBP) and knee pain. Overall, 915 individuals attended the weight management service from January 2011 to September 2015 [male, 35% (n = 318; confidence interval [CI] = 32-38); female, 65% (n = 597; CI = 62-68); mean age 44.6]. Mean body mass index was 50.7 kg/m2 [class III obese (body mass index ≥40 kg/m2), 92% (n = 835; CI = 91-94)]. Approximately 91% reported MSK pain: LBP, 69% (n = 539; CI = 65-72) [mean Numeric Rating Scale 7.4]; knee pain, 58% (n = 447; CI = 55-61) [mean Numeric Rating Scale 6.8]. Class III obese and multisite pain patients had lower QoL and physical activity levels, reduced sleep, and poorer physical function than less obese patients and those without pain (P < 0.05). Relationships were found between demographic, pain, self-report, psychological, and functional measures (P < 0.05). Patients who slept fewer hours and had poorer functional outcomes were more likely to have LBP; patients who were divorced, had lower QoL, and more frequent nocturia were more likely to have knee pain (P < 0.05). Multisite MSK pain is prevalent and severe in obese patients and is negatively associated with most self-report and functional outcomes. This high prevalence suggests that pain management strategies must be considered when treating obesity.