Science education is an essential element in thriving and surviving in a volatile, uncertain, complex, ambiguous, disruptive, and diverse (VUCAD 2 ) world. This cross-sectional research determines the challenges of junior high school students in learning science. A total of 123 junior high school students from four government-owned high schools in Zambales, Philippines, served as respondents of the study. Descriptive and inferential statistics were employed in analyzing the data. The developed Challenges in Learning Science Questionnaire (CLSQ) was used as the primary data gathering tool (α=0.95). Results revealed that junior high school students generally encounter not much challenges across all domains in learning science (M=2.06). However, based on the qualitative data, students encounter some issues and problems in learning the subject in terms of student motivation, student cognitive ability, teacher characteristics, subject matter content, medium of instruction, learning environment, instructional resources, curriculum and parental support. The t-test comparison revealed that male students encounter more challenges in terms of instructional resources and parental support compared to their female counterparts. The proposed action plan is crafted to minimize further the challenges encountered by the students in learning science. The teachers may consider varied and innovative pedagogical practices to explain better complex and complicated topics for better Science learning in a VUCAD 2 world.