Digitization is gradually penetrating all aspects of modern society. As it changes the way people communicate, technology has revolutionized education and training in the 21st century. With the advantages of reasonable costs and flexible study time, online training is increasingly seen as an attractive alternative to the full-time on-campus training model. To assure quality of distance training and learning, it is crucial for the online learning management system to make sure the person accessing the course resources and performing learning activities is actually enrolled in the course. One of the important factors determining the security of this process is user authentication. In most cases, this role is done with a password, but the evidence shows that this method is easily compromised. While there are many alternatives available such as biometric methods, user-challenging methods, smart card methods, etc. The strong development of technology that requires confidentiality and authentication must be tightly coupled. A qualitative survey of user authentication systems is being used in today's E-learning systems and a comparative study of various different authentication mechanisms presented in this paper. There are many methods of user authentication for online learning systems, but each method will have different advantages and disadvantages and has not completely solved the challenges of user authentication. The issue of user authentication still has many challenges that need to be solved thoroughly to improve the security of the system as well as the trust of users and society. This paper provides an overview of our approach and recommendations to address the mentioned issues. In addition, we propose a number of feasible approaches to improve user data privacy as well as improve the effectiveness of the authentication process in the online learning system.