The purpose of this study was to evaluate the role Inquiry-Based Learning (IBL) sequence delivered as Guided –Inquiry (GI) pedagogy for conceptual understanding of eighth-grade students in the concept of heat, in comparison with the Conventional Instruction (CI). A quasi-experimental pre/post-test design involves two groups, experimental and control groups were employed in this study. The sample students in the experimental and control groups were from the New Testament Christian Primary School (NTCPS) in Juba City, Central Equatorial State (CES)-South Sudan. These classes were taught by researcher at different time interval during the intervention period. There were 20 and 15 students in experimental and control group respectively. Guided inquiry pedagogical strategy which was designed with 5E instructional model employed for the experimental group students. Conventional instruction which was accompanied by more of traditional lecturing, except seldom question and answer, was applied for control group students. The two types of instructions run for almost two weeks, including the tutorial time. Open-ended conceptual test questions on the elementary heat concepts were applied to collect data before and after instructions. Furthermore interviews were conducted to selected students to obtain an in-depth understanding of the elementary heat conceptions held by the elementary eight grade students. The conceptual test scores were analyzed quantitatively using SPSS version 24 in order to calculate some relevance parameters of the data such as mean, standard deviation and variance.The findings of the study indicated that students were having little conceptions of heat concepts before instructions and have their conceptual knowledge improve after instructions in both experimental and control group as per the results of the analysis. The eighth grade pupils’ have much conception held by them after learning using conventional instruction on the concepts of elementary heat. The results also shows that the students who were taught using guided –inquiry have little conceptions of elementary heat and better in terms of their conceptual knowledge and misconceptions change in heat as better than before instruction. The results of the analysis indicated that guided-inquiry strategy was better than the conventional instruction and this is reflected in the computation of means using independent t-test in SSPS software. The interview data was analyses qualitatively as supplement to find out their feedback from both groups and it was incorporated in the general analysis of the data of post-test in both groups. The finding documented in this study provides evidence to generalize the effectiveness of guided inquiry pedagogical strategy for conceptual understanding of heat in elementary school contexts. It also recommended to teachers to apply guided inquiry pedagogical strategy in teaching the concept of heat for eighth grade students. Nevertheless, more studies in different countries, schools, school locations, and on various types of students should be investigated to further generalize the study.