The novel coronavirus disease (COVID-19) pandemic has affected the basic education sector in the Philippines. In the public school system, the pandemic has not only disrupted schooling by shifting the beginning of the school year (SY) 2020-20201 at a later time, it has also necessitated a shift to alternative learning delivery strategies, including the use of more flexible face-to-face, distance and blended learning. This paper focuses on the effects of the COVID-19 outbreak on the K to 12 senior high school (SHS) program and the need to offer flexible learning options (FLOs) to upper secondary learners. It examines the policies the Department of Education (DepEd) has initiated in continuing learning during the pandemic and providing education through FLOs using the INEEs domain standards on EiE. From this policy analysis, the paper identified some gaps that need to be addressed through the following recommendations 1) intensify FLO guidelines to meet the different needs and contexts of learners, especially the marginalized; 2) develop an EiE policy; 3) improve teaching-learning by strengthening communication channels, formative assessment, and multimedia learning materials; 4) provide offline and online options for SHS tracks; 5) explore the use of videos, mobile training centers and flexible times of study.