The study used causal-comparative research design to examine the scientific literacy among randomly selected Junior High School students under the Science, Technology and Engineering Program (STEP) of a National High School in the Philippines. Specifically, it investigated the factors that facilitate and hinder the students' ability to write and present scientific research. Quantitative and qualitative data were gathered from primary and secondary sources. Descriptive statistics were used to analyse the data obtained from the interviews and questionnaires. Findings showed that the scientific literacy of students in terms of writing was perceived as good while presenting the scientific research was described as fair. The study also revealed that teachers' factors, learning environment, and school administrative support affect the scientific literacy skills development of the students. Thus, the study suggested that by promoting the identified factors, the scientific literacy skills of the students will be further developed. Additionally, increase of teacher's availability during consultation hours, use of differentiated instructions, localization, contextualization, formulation of policy guidelines for the use of learning resources, plan of activities for STEP, as well as development of a module, research networks and linkages should be given importance.