Learners' well-being plays a role in shaping academic outcomes and is vital for an educational institution to look into. The study aimed to describe the well-being and assessed the relationship of academic performance of secondary learners in their National Achievement Test in Mathematics, Science, Filipino, Araling Panlipunan and English. Data were collected using descriptive-correlational methods to describe and assess the well-being dimensions of the students. The learners' academic performance and well-being are significantly related in five key areas, but not significantly related to their physical, social, and material well-being. The well-being dimensions of learners in terms of cognitive, psychological, physical, social, and material had no significant extent on their Mathematics, Science, Filipino, English, and Araling Panlipunan performance. However, the psychological well-being dimension of the learners had a significant extent on their overall academic performance. The study concludes that students should be given proper attention, particularly learners with low psychological well-being. It is recommended that school needs to design continuous programs to help these learners have a sense of control and prevent them from being completely consumed by emotional reactions.