Anorexia nervosa (AN) and bulimia nervosa (BN) are eating diseases characterized by extreme eating behaviours impacting both mental and physical health. Aberrant musculoskeletal adaptations due to malnutrition affect motor abilities such as postural control and gait. To date, limited data is available with regards to gait symmetry in AN and BN. The aim of this study was to characterize inter-limb asymmetry during gait in two cohorts affected by AN and BN, respectively, using the synchronized cyclograms and to compare it with a healthy weight group. A total of 14 AN, 17 BN, and 11 healthy-weight females were assessed via 3D gait analysis. Gait spatio-temporal parameters were computed together with angle–angle diagrams, which were characterized in terms of their geometric features. Individuals with AN and BN were characterized by reduced speed and cadence and an abnormal increase in the duration of the double support phase with respect to the healthy controls. With respect to inter-limb symmetry, asymmetries were detected in both groups, with individuals with BN exhibiting significantly larger cyclogram areas at the hip joint with respect to the other groups (323.43 degrees2 vs. 253.74 degrees2 vs. 136.37 degrees2) and significantly higher orientation angle and Trend Symmetry at both knee and ankle joint. The cyclogram analysis suggests the presence of an altered gait symmetry in individuals with BN. In the AN group, it is possible to observe a similar trend; however, this is not statistically significant. Overall, the findings of this study may provide a novel perspective on the motor control dysfunction linked to eating disorders and aid clinicians in selecting a suitable rehabilitation scheme targeted at enhancing motor stability and control.