Quarantines and virtual learning became necessary as a result of the COVID-19 pandemic. This study investigates the challenges and opportunities in virtual classes; and how they affect the academic goals. There were 150 secondary students from Junior and Senior High School levels of education in the Philippines, who were deliberately selected; and they participated in the quantitative online survey that used a 62-item self-made 4-point Likert scale questionnaire, with 0.81 reliability coefficients. The data were evaluated by means of the percentage, the mean, and the standard deviation. Sex and secondary education levels were used, in order to compare the students’ challenges and opportunities. One-way ANOVA compared the male and female respondents’ perceived challenges and opportunities. The results revealed that junior high-school (JHS) girls highlighted academic satisfaction; while school-life balance, and virtual learning helped as challenges and opportunities. The females found school-life balance, communication (F(1,149)=11.098; F(1,149)=8.430, p<0.01), academic fulfilment, self-directedness, and time-management (F(1,149)=4.224; F(1,149)=4.470; F(1,149)=4.030, p<0.05) more difficult than did the males. Senior high school (SHS) students were less satisfied with the virtual teaching (F(1,149)=14.391, p<0.001), technology use (F(1,149)=7.342, p<0.01), and communication (F(1,149)=3.934, p<0.05) than JHS students. Males were more satisfied with school and teachers’ assistance (F(1,149)=7.482, p<0.01). Some viewed virtual learning more favourably; and they regard themselves as being adaptive; they think the subject matter and learning tasks are interrelated; and they viewed virtual feedback more positively (F(1,149)=6.438; F(1,149)=5.900; F(1,149)=5.183; F(1,149)=4.470, p<0.05). The JHS students reported subject matter and the virtual learning tasks as being interrelated; and they valued virtual feedback, school and teacher support, and the adaptability to change. Challenges and opportunities may serve as the foundation for establishing a more inclusive policy on virtual learning implementation, with school and stakeholders’ cooperation needed to sustain learners’ holistic development.
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