Background: A large number of students enrolled in many universities and the low ratio of supervisors to the student have challenged the process of developing education and research. Today, information and communication technology (ICT) tools have changed the learning environments. We assessed the improvement in challenges in the thesis process for Master’s degree virtual students using learning management systems (LMS). Methods: This study is a translational research design focusing on adaptation of educational technology and was conducted in three stages: Preparation, implementation, and assessment in the Shahid Beheshti University of Medical Sciences in 2017. In the preparation stage, we matched LMS with technical support requirements. In the experimental stage, the effectiveness of a web-based system (LMS) for thesis support was assessed in 67, 65, and 51 master students in 2017, 2018, and 2019, respectively, and they were followed two years. In the post- experimental stage, the program was assessed using quality criteria. The data were analyzed by descriptive statistics (mean and standard deviation), analysis of variance (ANOVA), and post-hoc tests. Results: Data of 67 students as the first entry group were collected after two years of implementation of the program and 22 quality criteria were extracted by literature review and validated by focus group discussion. The results of students’ perspective showed that the scores of the quality criteria after using LMS in comparison other alternative methods were at the desirable level (mean score > 7), the social network and email scores were mostly at the moderate level, and the meeting was almost less desirable (mean score < 4). The results of the supervisors’ perspective also showed that the scores of the quality criteria were at the desirable level. The ANOVA result for most criteria was statistically significant at 95% CI. The results indicated the higher scores in all quality criteria after using LMS in comparison with alternative methods from the viewpoints of the supervisors and students (95% CI: 8.76 ± 0.83) and (95% CI: 8.71 ± 0.64), respectively. Conclusions: The results of this study indicated that implementing LMS for thesis support was almost twice more successful in achieving the considered criteria than other alternative methods in terms of both students’ and supervisors’ perspectives. Implementation of LMS in the thesis process, which significantly affects the quality and quantity of research through improvement in feedback quality, saves time, and increases the rate of thesis completion.