Subject-specific musculoskeletal modelling is especially useful in the study of juvenile and pathological subjects. However, such methodologies typically require a human operator to identify key landmarks from medical imaging data and are thus affected by unavoidable variability in the parameters defined and subsequent model predictions. The aim of this study was to thus quantify the inter- and intra-operator repeatability of a subject-specific modelling methodology developed for the analysis of subjects with juvenile idiopathic arthritis. Three operators each created subject-specific musculoskeletal foot and ankle models via palpation of bony landmarks, adjustment of geometrical muscle points and definition of joint coordinate systems. These models were then fused to a generic Arnold lower limb model for each of three modelled patients. The repeatability of each modelling operation was found to be comparable to those previously reported for the modelling of healthy, adult subjects. However, the inter-operator repeatability of muscle point definition was significantly greater than intra-operator repeatability (p < 0.05) and predicted ankle joint contact forces ranged by up to 24% and 10% of the peak force for the inter- and intra-operator analyses, respectively. Similarly, the maximum inter- and intra-operator variations in muscle force output were 64% and 23% of peak force, respectively. Our results suggest that subject-specific modelling is operator dependent at the foot and ankle, with the definition of muscle geometry the most significant source of output uncertainty. The development of automated procedures to prevent the misplacement of crucial muscle points should therefore be considered a particular priority for those developing subject-specific models.