This study aimed to investigate the level of student engagement in online courses in the Instructional and Learning Technologies department (ILT) at SQU during the Covid-19 pandemic. The study also explored the challenges that impeded student engagement in online courses. The study followed a descriptive design using a purposive sample of 111 students and five instructors. Mixed methods were used for gathering the data of the study. The level of student engagement was measured through the survey of student engagement and the analysis of the MOODLE reports. Moreover, semi-structured interviews were conducted with six students and five instructors to investigate the challenges that hindered student engagement. Although, the study revealed some challenges that impeded the student engagement in online courses like: heavy workload on students, students' inability to manage their study time, low-level of class participation, increase of instructors' burdens. The findings of the study indicated that the ILT undergraduate students still showed a high level of engagement. Thus, the revealed challenges would help the educators to plan in advance for better strategies for student engagement. The study presented some recommendations and avenues for further research.