This study examined the difficulties of running online physical education classes in the context of coronavirus disease 2019 (COVID-19) and used the findings to develop an efficient operation plan to address these difficulties. Six middle and high school physical education teachers participated; three were experts in online physical education and active in the Korea Council School Physical Education Promotion, and three were recommended teachers making efforts to improve the online classes offered by the Korea Ministry of Education. A qualitative case study method employing phenomenological procedures to collect and analyze the data was used. The difficulties of operating middle and high school online physical education classes for the first time included (1) the monotony of the classes within their limited environmental conditions and limited educational content that did not adequately convey the value of physical education, (2) trial-and-error methods applied nationwide, resulting from a lack of expertise in operating online physical education classes, and (3) very limited evaluation guidelines proposed by the Korea Ministry of Education, which made systematic evaluation with online methods impossible. To address the identified problems and facilitate the efficient operation of online physical education classes, changes in strategic learning methods are needed to understand online physical education characteristics and thereby better communicate the value of physical education. It is also necessary to cultivate teaching expertise through sharing online physical education classes, where collaboration among physical education teachers is central. In addition, evaluation processes should be less formal to encourage active student participation.