Prioritizing well-being is one way to nurture the cognitive development of learners. The study aimed to evaluate the well-being of secondary learners in terms of cognitive, psychological, physical, social, and material dimensions. Also, this study determines the academic performance of learners in their subject grades/GPA and National Achievement Test. Using descriptive-correlational and causal research design, this study was participated by 1,609 learners from selected schools of the City Divisions of Bukidnon, Philippines. A modified PISA well-being questionnaire (2016) was used and undergoes content and face validity through Delphi and pilot testing with Cronbach Alpha of .792. The study results revealed that all dimensions are positively professed as vital in students' well-being; however, the social dimension is less likely to be addressed among the five factors. Also, only four well-being dimensions, namely; cognitive, psychological, social, and material dimensions, are significantly highly correlated to learners' academic performance with R-values of 0.240, 0.230, 0.082, and 0.184, respectively. One of the ultimate goals of this study is to develop an intervention program for well-being and performance of learners through causal modelling.