Abstract Background Despite advancements in the pharmacological management of early rheumatoid arthritis (RA), walking impairments remain a key feature of this disease. With limited published research analysing the impact of early RA on lower limb movement patterns during gait, more comprehensive data are required to optimise the recognition and targeted management of early musculoskeletal pathology in RA. This study compared lower limb biomechanical function in early RA participants to age and gender-matched healthy controls, determining explanatory relationships with measures of disease activity and physical function. Methods In a cross-sectional study using three-dimensional (3D) motion capture, lower limb kinematic data from 18 RA participants with disease duration ≤ 2 years were compared to 18 adults matched for age and gender. Standard clinical measures were used to collect data on disease activity, rheumatology physical function and self-reported physical impairment. Between-group differences in lower limb kinematics were investigated using principal component analysis (PCA). Explanatory variables of significantly altered lower limb kinematics in early RA were investigated using linear regression analysis. Results Of the lower limb parameters analysed, eversion of the rearfoot and midfoot were found to be significantly increased (p < 0.05) in early RA, with two principal components explaining 91.94% and 97.57% of the respective between-group variance. Rearfoot motion in early RA was explained by single regression models incorporating walking speed (R2 of 0.456, F ratio = 12.585, p = < 0.003), the footwear/impairment domain of the Leeds Foot Impact Scale (R2 = 0.358, F ratio = 8.371, p = <0.011) and rheumatoid factor (R2 = 0.358, F ratio = 8.371, p = <0.011). Midfoot eversion was explained by single regression models incorporating the timed walk test (R2 = 0.372, F ratio = 4.507, p = < 0.031), the percentage of gait at which toe-off occurred (R2 of 0.253, F ratio = 5.425, p = < 0.033) and walking speed (R2 = 0.235, F ratio = 4.912, p = < 0.042). Abduction of the rearfoot and midfoot were also significantly increased (p < 0.05) in early RA. Two principal components explained 97.67% and 97.2% of the respective between-group variance observed. No variables were found to explain altered motion at these sites. Dorsiflexion at the first metatarsophalangeal joint (MPJ) was significantly reduced (p < 0.05) in early RA, with a single principal component explaining 97.43% of between-group variance which was explained by a single regression model incorporating step length (R2 = 0.372, F ratio = 4.507, p = <0.031). Conclusion Within two years following diagnosis of RA, significant alterations in foot kinematics were observed despite management using current treat to target protocols. These alterations were of a greater magnitude than previously reported and were largely independent of current measures of disease activity, physical function and disease impact. Disclosures A.G. Izod Grants/research support; Dr William Scholl Research and Develpment Fund. C. Bowen None. K. Gallagher None. M. Seed None.