The COVID-19 Pandemic has led Higher Education Institutions (HEIs) in the Philippines to replace on-campus learning with flexible learning. This paper explores the students' challenges on flexible online learning implementation of the university in the rural area based on their background and experience. This employed quantitative and qualitative methods through a survey and an interview respectively sought to gather data from 639 university students. Data were analyzed with descriptive statistics and narrative analysis. Results revealed that most mothers are high school graduates, while fathers enjoy an elementary-level and belong to under low-income families. Most students possess just mobile phones and use mobile data as their primary internet access source, ranging from moderate to poor connection. Also, the majority are not fully equipped with enough skills in digital media. For challenges, students experienced the unavailability of a network, economic instability, digital divide, the shortage of digital devices, distractive learning environment, expensive internet data, health-related problems, lack of resources, lack of digital literacy skills, and loss of motivation .Hence, even if flexible online learning is the best solution for the university to replace face-to-face classes, it is not best applicable and suitable to all students living in rural areas or other places with an unstable network and students who belong to financially unstable families. Administrators and educators have to consider alternative learning modes that suit students' backgrounds during the pandemic, like using non-digital technologies.