The global outbreak of COVID-19 posed significant challenges to educational systems. The shift to distance learning underscored the crucial importance of self-directed learning. The study was to determine the mediating effect of motivation factors in the relationship between science anxiety and self-directedness on modular learning in the science of Grade 10 students of public secondary junior high schools in Mabini District, Davao de Oro Division. This research used descriptive and correlational designs, to determine the relationships between variables.Then stratified random sampling was employed, and 300 respondents were chosen from the three public secondary junior high schools to be interviewed. Two adopted questionnaires, The Anxiety Scale (SAS) and Students Motivation toward Science Learning Survey (SMTSL), and one adopted questionnaire, the Self-Directed Learning Readiness Scale (SLRS), were used as tools in gathering substantial data. The mean with standard deviation, person r, and Sobel tests were used as statistical tools. This study revealed students’ science anxiety to be at a moderate level, while both students’ motivation factors and self directedness were high. Furthermore, science anxiety was not significantly related to motivation factors and self-directedness. On the other hand, the relationship between motivation factors and self-directedness was significant. It was found that motivational factors have no significant mediating effect on the relationship between science anxiety and the self-directedness of the students under modular distance learning in science. The results of the study would benefit the students, teachers, school administrators, DepEd officials, and other researchers in effectively teaching science subject to junior high school students.