In this paper we consider the application of online course “Neural Network modeling of Complex Technical Systems” in the Master’s degree programs in the field of nanotechnology and nanoengineering in Bauman Moscow State Technical University. The course has rather practical than theoretical nature. The aim of this course is skill oriented learning. Nowadays neural network models have become a powerful tool of scientific research for engineers and students. The methods studied during the study of the discipline can be applied to estimation, modeling, classification, clustering, forecasting and more. The neural networks modeling plays a significant role in Master’s education and student’s research work. Neural Networks models are successfully presented in graduation theses. Thanks to online educations students can practice at their own pace and study modern neural networks software products, methods of data preparing, designing and training neural network and then apply these algorithms in practice. According to the steps of neural network modeling algorithm the course consists of three main parts and conclusive one. In this paper course structure and study results are presented.