Forecasted gait trajectories of children could be used as feedforward input to control lower limb robotic devices, such as exoskeletons and actuated orthotic devices (e.g., Powered Ankle Foot Orthosis-PAFO). Several studies have forecasted healthy gait trajectories, but, to the best of our knowledge, none have forecasted gait trajectories of children with pathological gait yet. These exhibit higher inter- and intra-subject variability compared to typically developing gait of healthy subjects. Pathological trajectories represent the typical gait patterns that rehabilitative exoskeletons and actuated orthoses would target. In this study, we implemented two deep learning models, a Long-Term Short Memory (LSTM) and a Convolutional Neural Network (CNN), to forecast hip, knee, and ankle trajectories in terms of corresponding Euler angles in the pitch, roll, and yaw form for children with neurological disorders, up to 200 ms in the future. The deep learning models implemented in our study are trained on data (available online) from children with neurological disorders collected by Gillette Children's Speciality Healthcare over the years 1994-2017. The children's ages range from 4 to 19 years old and the majority of them had cerebral palsy (73%), while the rest were a combination of neurological, developmental, orthopaedic, and genetic disorders (27%). Data were recorded with a motion capture system (VICON) with a sampling frequency of 120 Hz while walking for 15 m. We investigated a total of 35 combinations of input and output time-frames, with window sizes for input vectors ranging from 50-1000 ms, and output vectors from 8.33-200 ms. Results show that LSTMs outperform CNNs, and the gap in performance becomes greater the larger the input and output window sizes are. The maximum difference between the Mean Absolute Errors (MAEs) of the CNN and LSTM networks was 0.91 degrees. Results also show that the input size has no significant influence on mean prediction errors when the output window is 50 ms or smaller. For output window sizes greater than 50 ms, the larger the input window, the lower the error. Overall, we obtained MAEs ranging from 0.095-2.531 degrees for the LSTM network, and from 0.129-2.840 degrees for the CNN. This study establishes the feasibility of forecasting pathological gait trajectories of children which could be integrated with exoskeleton control systems and experimentally explores the characteristics of such intelligent systems under varying input and output window time-frames.