By the beginning of 2020, there were widespread school closures caused by the spread of coronavirus for an unknown duration. Consequently, many schools turned to online learning using a software application, or a video conferencing system. As high levels of self-directed learning (SDL) are important for the quality of online learning, the present study aimed to understand learner SDL in an online environment and identify its challenges and barriers at one of the higher education institutes in Oman. It addressed a case study that documented how learning went in three online courses and reported perceptions of learners pertaining to effective SDL. Data were collected through interviews with seven selected students from each course, virtual observations of online teaching, and course documents. Results revealed four issues related to students' SDL in online classes: (1) student cognitive engagement with online learning, (2) student-centered approach, (3) time-management and (4) student emotional engagement with online learning. The findings suggest a need to design an effective online learning environment through reinforcing students' satisfaction and motivation in online classes, their time management skill, a student-centered approach and teacher presence.