Security in e-learning system becomes a fundamental requirement. Because e-learning systems increase in popularity, the need to understand security will also increase. It is important to ensure that all information within the e-learning environment is properly protected; by addressing the security requirements in e-learning systems for the three main processes, which are creating content, (teaching and learning) and organization. A framework for e-learning system security is designed to capture the security requirements, which contains the definitions, user's view of learning operation, the assumptions. Moodle has been chosen as a case study to develop its security systems such as access control (roles and permissions), authentication and (backup and recovery). The framework is proposed to implement at Sudan University of Science & Technology using the learning management system - Moodle.