Background Robot-assisted gait therapy is increasingly being used in pediatric neurorehabilitation to complement conventional physical therapy. The robotic device applied in this study, the Lokomat (Hocoma AG, Switzerland), uses a position control mode (Guidance Force), where exact positions of the knee and hip joints throughout the gait cycle are stipulated. Such a mode has two disadvantages: Movement variability is restricted, and patients tend to walk passively. Kinematic variability and active participation, however, are crucial for motor learning. Recently, two new control modes were introduced. The Path Control mode allows the patient to walk within a virtual tunnel surrounding the ideal movement trajectory. The FreeD was developed to support weight shifting through mediolaterally moveable pelvis and leg cuffs. The aims of this study were twofold: 1) To present an overview of the currently available control modes of the Lokomat. 2) To evaluate if an increase in kinematic variability as provided by the new control modes influenced leg muscle activation patterns and intensity, as well as heart rate while walking in the Lokomat. Methods In 15 adolescents with neurological gait disorders who walked in the Lokomat, 3 conditions were compared: Guidance Force, Path Control, and FreeD. We analyzed surface electromyographic (sEMG) activity from 5 leg muscles of the more affected leg and heart rate. Muscle activation patterns were compared with norm curves. Results Several muscles, as well as heart rate, demonstrated tendencies towards a higher activation during conditions with more kinematic freedom. sEMG activation patterns of the M.rectus femoris and M.vastus medialis showed the highest similarity to over-ground walking under Path Control, whereas walking under FreeD led to unphysiological muscle activation in the tested sample. Conclusions Results indicate that especially Path Control seems promising for adolescent patients undergoing neurorehabilitation, as it increases proximal leg muscle activity while facilitating a physiological muscle activation. Therefore, this may be a solution to increase kinematic variability and patients’ active participation in robot-assisted gait training. Electronic supplementary material The online version of this article (doi:10.1186/s12984-017-0287-1) contains supplementary material, which is available to authorized users.