Knee pain is an important health problem due to its high prevalence, negative impact on daily activities and quality of life, and societal burden. While the link between excess weight and knee pain has been well-documented in the literature, many studies are limited to patients with osteoarthritis or use cross-sectional data. This longitudinal study investigated whether overweight and obesity were associated with the frequency and severity of frequent knee pain (FKP) episodes over 4 years in civil servants enrolled in the ELSA-Brasil MSK cohort. Knee pain was assessed during baseline face-to-face interviews (2012-2014) and four yearly telephone follow-ups (2015-2019). Disabling FKP episodes or those of moderate to very severe intensity were classified as severe. Multinomial logistic regression models adjusted for confounders were used to test for associations in two participant groups: those with knee pain at baseline (prognosis cohort) and those without knee pain (incidence cohort). A total of 2644 participants were included: 54.2% female, mean age 55.8 (SD 8.8) years. In the incidence cohort (n = 1896), obesity increased the risk of one (OR: 1.63; 95% CI 1.13-2.37) and multiple FKP episodes (OR: 2.61; 95% CI 1.71-3.97), as well as the risk of non-severe (OR: 1.72; 95% CI 1.04-2.84) and severe FKP episodes (OR: 2.10; 95% CI 1.50-2.95). In the prognosis cohort (n = 748), obesity increased the risk of multiple (OR: 2.54; 95% CI 1.60-4.05) and severe FKP episodes (OR: 2.31; 95% CI 1.49-3.59). Overweight presented the same trends but fell short of significance. These results provide further support that overweight and obesity are important contributors to the incidence and worsening of FKP, and that weight management must be prioritized in multidisciplinary knee pain prevention and treatment programs to reduce the burden of musculoskeletal disorders.