In response to the COVID-19 pandemic, Jordan declared a state of emergency on 19 March 2020, implementing a 10-week curfew and closing all educational institutions. Consequently, online learning commenced to ensure educational continuity amid the pandemic. The aim of this study was to assess medical students’ perception of online teaching during this period in a limited-resource setting and to identify associated challenges. A cross-sectional survey was conducted involving 393 undergraduate medical students in their 4^th, 5^th, and 6^th year from six universities across Jordan. The self-administered online survey included four categories, exploring the satisfaction of medical students and challenges they faced during online education, and was distributed on Facebook and WhatsApp. A total of 393 students completed the survey, 264 (62.6%) of which were female. The majority of respondents were from Jordan University and in their 4^th year. Regarding online teaching, 218 (55.5%) expressed satisfaction; however, an equivalent percentage disagreed that online methods could replace traditional teaching. Notably, 238 (86%) believed that their confidence in new clinical skills acquired through online education was adversely affected. The study highlights the need for targeted interventions to improve the effectiveness of online education, especially in developing essential clinical skills.