Teaching Science in a digital society where 21st century skills are being harnessed is a perennial challenge. This is for the reason that teachers, specifically in the elementary level, are relentlessly modifying and innovating teaching strategies to improve science education. This action research study sought to explore the effects of Sci-vestigative Pedagogical Strategy (SPS) on the conceptual understanding on Matter of Grade 6 Science pupils. The study involved 29 pupils in the control group and 30 pupils in the experimental group in a public elementary school in the Division of Zambales for the School Year 2018-2019. Pre-test and post-test were administered before and after the application of the intervention to measure its effects on the conceptual understanding on matter of the pupils. The study found out that there was a significant difference in the conceptual understanding of the pupils in the experimental and control group. However, the use of SPS yielded a higher gain score compared to the gain score in the use of traditional method of instruction (TMI). The pupils' written works and performance tasks scores have also improved with the use of the SPS. The study recommends that Science teachers may use SPS to improve pupils' conceptual understanding including their concepts and content knowledge; depth within topics; and transfer and connections and to develop their higher order thinking and inquiry skills. School administrators may consider conducting training and workshops for Science teachers to reacquaint them of the basic rudiments of the Sci-vestigative Pedagogical Strategy which is based on inquiry-based learning. Students may be given varied roles in the agham (science) inquiry tasks so that they can better work as a group. A parallel study may be conducted by other teacher-researchers to validate the effects of the intervention in enhancing pupils' conceptual understanding in other topics.